Command coverage

turbo-picard exposes the full Picard 3.4.0 command surface. Accelerated commands run natively in Rust when possible; every other Picard 3.4.0 command is delegated transparently to upstream Picard when it is installed or auto-discovered.

List every upstream command with:

turbo-picard --list-commands

Common command examples

These examples cover the accelerated preprocessing and QC path. Check the machine-readable matrix below for the exact accelerated versus delegated split.

picard MarkDuplicates I=input.bam O=marked.bam M=metrics.txt
picard SortSam I=input.bam O=coordinate.bam SORT_ORDER=coordinate
picard CleanSam I=input.bam O=cleaned.bam
picard MergeSamFiles I=lane1.bam I=lane2.bam O=merged.bam SORT_ORDER=coordinate
picard BuildBamIndex I=coordinate.bam O=coordinate.bai
picard SamToFastq I=input.bam FASTQ=r1.fastq SECOND_END_FASTQ=r2.fastq
picard SamToFastq I=input.bam OUTPUT_PER_RG=true OUTPUT_DIR=fastq-by-rg
picard FastqToSam F1=r1.fastq F2=r2.fastq O=unmapped.bam SM=sample RG=rg1
picard FastqToSam F1=reads_R1_001.fastq F2=reads_R2_001.fastq O=unmapped.bam SM=sample RG=rg1 USE_SEQUENTIAL_FASTQS=true
picard ViewSam I=input.bam > view.sam
picard ReplaceSamHeader I=input.bam O=reheadered.bam H=replacement-header.sam
picard AddOrReplaceReadGroups I=input.bam O=rg.bam RGID=1 RGLB=lib RGPL=ILLUMINA RGPU=unit RGSM=sample
picard CollectAlignmentSummaryMetrics I=input.bam O=alignment_metrics.txt
picard CollectQualityYieldMetrics I=input.bam O=quality_yield_metrics.txt
picard CreateSequenceDictionary R=reference.fa O=reference.dict
picard NormalizeFasta I=reference.fa O=normalized.fa LINE_LENGTH=100
picard BedToIntervalList I=targets.bed O=targets.interval_list SD=reference.dict
turbo-picard AccelerationStatus
turbo-picard doctor
turbo-picard explain MarkDuplicates I=input.bam O=marked.bam M=metrics.txt
turbo-picard explain --json MarkDuplicates I=input.bam O=marked.bam M=metrics.txt
turbo-picard explain --format json MarkDuplicates I=input.bam O=marked.bam M=metrics.txt

Use the text explain output for interactive checks. Use --json when a workflow wrapper, CI check, or platform module needs to read schema_version, command status, execution path, fallback command, and declared output arguments without parsing human text.

Metrics and repair examples

picard QualityScoreDistribution I=input.bam O=quality_distribution.txt CHART=quality_distribution.pdf
picard MeanQualityByCycle I=input.bam O=mean_quality_by_cycle.txt CHART=mean_quality_by_cycle.pdf
picard CollectBaseDistributionByCycle I=input.bam O=base_distribution.txt CHART=base_distribution.pdf
picard CollectInsertSizeMetrics I=input.bam O=insert_size_metrics.txt H=insert_size_histogram.pdf
picard CollectGcBiasMetrics I=input.bam O=gc_bias_detail.txt S=gc_bias_summary.txt CHART=gc_bias.pdf R=reference.fa
picard CollectHsMetrics I=input.bam O=hs_metrics.txt BAIT=baits.interval_list TARGET=targets.interval_list R=reference.fa
picard CollectMultipleMetrics I=input.bam O=multiple_metrics PROGRAM=CollectInsertSizeMetrics
picard CollectWgsMetrics I=input.bam O=wgs_metrics.txt R=reference.fa COUNT_UNPAIRED=true
picard CollectWgsMetrics I=input.bam O=wgs_metrics.fast.txt R=reference.fa COUNT_UNPAIRED=true USE_FAST_ALGORITHM=true
picard FixMateInformation I=queryname.bam O=fixed.bam ASSUME_SORTED=true SORT_ORDER=queryname
picard RevertSam I=aligned.bam O=unmapped.bam
picard SetNmMdAndUqTags I=coordinate.bam O=tagged.bam R=reference.fa
picard ValidateSamFile I=input.bam MODE=SUMMARY

VCF and interval examples

picard UpdateVcfSequenceDictionary I=input.vcf O=updated.vcf SD=reference.dict CREATE_INDEX=true
picard GatherVcfs I=shard1.vcf I=shard2.vcf O=gathered.vcf CREATE_INDEX=true
picard SortVcf I=unsorted.vcf O=sorted.vcf SD=reference.dict CREATE_INDEX=true
picard MergeVcfs I=batch1.vcf I=batch2.vcf O=merged.vcf CREATE_INDEX=true
picard LiftoverVcf I=input.vcf O=lifted.vcf CHAIN=build.chain REJECT=rejected.vcf R=target.fa
picard IntervalListTools I=a.interval_list I=b.interval_list O=merged.interval_list ACTION=CONCAT SORT=true UNIQUE=true

Machine-readable coverage

The canonical command matrix lives in docs/command-matrix.yml. It records the current status, parity script, native scope, and fallback scope for each Picard 3.4.0 command plus turbo-only utilities such as AccelerationStatus, doctor, and explain.

Current matrix status summary:

  • 35 accelerated commands with native or partial-native Rust implementations

  • 89 delegated Picard 3.4.0 commands forwarded to upstream Picard

Accelerated command status:

  • AddOrReplaceReadGroups: native

  • AccelerationStatus: native

  • BedToIntervalList: native

  • BuildBamIndex: native

  • CleanSam: partial-native

  • CollectAlignmentSummaryMetrics: partial-native

  • CollectBaseDistributionByCycle: partial-native

  • CollectGcBiasMetrics: partial-native

  • CollectQualityYieldMetrics: native

  • CollectWgsMetrics: partial-native. INCLUDE_BQ_HISTOGRAM defaults to false to match Picard 3.4.0 histogram output. USE_FAST_ALGORITHM=true stays native and defaults SAMPLE_SIZE to 0 unless it is set explicitly. TURBO_PICARD_WGS_FAST_DEFAULT=true applies that sample-size default when the command line does not set USE_FAST_ALGORITHM.

  • doctor: native

  • explain: native

  • CreateSequenceDictionary: native

  • FastqToSam: partial-native

  • GatherVcfs: partial-native

  • MarkDuplicates: partial-native

  • MergeSamFiles: partial-native

  • MergeVcfs: partial-native

  • MeanQualityByCycle: partial-native

  • NormalizeFasta: native

  • QualityScoreDistribution: partial-native

  • ReplaceSamHeader: partial-native

  • SamToFastq: partial-native

  • SortSam: partial-native

  • SortVcf: partial-native

  • UpdateVcfSequenceDictionary: partial-native

  • ViewSam: partial-native

  • CollectInsertSizeMetrics: partial-native

  • CollectMultipleMetrics: partial-native

  • FixMateInformation: partial-native

  • IntervalListTools: partial-native

  • LiftoverVcf: partial-native

  • RevertSam: partial-native

  • SetNmMdAndUqTags: partial-native

  • ValidateSamFile: partial-native

picard_reference: "3.4.0"
commands:
  - name: AccelerationStatus
    status: native
    parity_script: tools/verify_basic_accelerationstatus_parity.sh
    native_scope: "turbo-picard utility command that reports the effective CPU accelerator policy, HTSlib worker-thread count, detected GPU runtime, and fails when TURBO_PICARD_ACCELERATOR=gpu-required is set without a production GPU backend."
    fallback_scope: This is not an upstream Picard command and does not delegate to fallback.
  - name: AccumulateQualityYieldMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: AccumulateVariantCallingMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: AddCommentsToBam
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: AddOATag
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: AddOrReplaceReadGroups
    status: native
    parity_script: tools/verify_basic_addorreplacereadgroups_parity.sh
    native_scope: "SAM/BAM/CRAM read-group replacement with REFERENCE_SEQUENCE for CRAM paths, Picard-style RG fields including key sequence and flow order, per-record RG tag rewrite, .md5 sidecars, BAM indexing when requested, common Picard runtime option acceptance, and GATK NA12878 mitochondrial real-data parity."
    fallback_scope: "No known fallback-only behavior in the current documented implementation."
  - name: BaitDesigner
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: BamIndexStats
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: BamToBfq
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: BedToIntervalList
    status: native
    parity_script: tools/verify_basic_bedtointervallist_parity.sh
    native_scope: "BED to interval-list conversion with dictionary-order sorting by default, UNIQUE handling, DROP_MISSING_CONTIGS skipping, Picard-compatible zero-length interval handling, common no-op runtime sidecar options, and SORT=false input-order output with coordinate header."
    fallback_scope: "No known fallback-only behavior in the current documented implementation."
  - name: BpmToNormalizationManifestCsv
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: BuildBamIndex
    status: native
    parity_script: tools/verify_basic_buildbamindex_parity.sh
    native_scope: "BAI generation for coordinate-sorted BAM inputs with default or explicit output paths, Picard-compatible CREATE_MD5_FILE acceptance without an index md5 sidecar, and GATK NA12878 mitochondrial real-data parity."
    fallback_scope: "Non-BAM inputs are delegated when fallback is configured."
  - name: CalculateFingerprintMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CalculateReadGroupChecksum
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CheckDuplicateMarking
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CheckFingerprint
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CheckIlluminaDirectory
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CheckTerminatorBlock
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CleanSam
    status: partial-native
    parity_script: tools/verify_basic_cleansam_parity.sh
    native_scope: "Common SAM/BAM/CRAM cleanup with REFERENCE_SEQUENCE for CRAM paths, including unmapped MAPQ normalization, simple reference-overhang clipping, terminal deletion/reference-overhang clipping matched to Picard, and release-candidate real-data parity."
    fallback_scope: "Complex reference-edge cases outside the native cleaner should use upstream Picard."
  - name: ClusterCrosscheckMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectAlignmentSummaryMetrics
    status: partial-native
    parity_script: tools/verify_basic_alignmentmetrics_parity.sh
    native_scope: "No-reference ALL_READS, SAMPLE, LIBRARY, and READ_GROUP alignment summary metrics for SAM/BAM/CRAM with REFERENCE_SEQUENCE for CRAM paths, plus read-length histogram and release-candidate real-data parity."
    fallback_scope: "Reference-dependent mismatch, error-rate, and adapter-oriented metrics remain upstream Picard cases."
  - name: CollectArraysVariantCallingMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectBaseDistributionByCycle
    status: partial-native
    parity_script: tools/verify_basic_collectbasedistributionbycycle_parity.sh
    native_scope: Base percentage by cycle metrics and lightweight PDF chart artifact for common SAM/BAM/CRAM inputs with REFERENCE_SEQUENCE for CRAM paths.
    fallback_scope: Advanced charting semantics and unsupported Picard options should use fallback.
  - name: CollectDuplicateMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectGcBiasMetrics
    status: partial-native
    parity_script: tools/verify_basic_collectgcbiasmetrics_parity.sh
    native_scope: "GC-bias detail, summary, optional duplicate-filtered metrics, and lightweight PDF chart artifact for reference-backed SAM/BAM/CRAM runs."
    fallback_scope: Bisulfite mode and unsupported accumulation/window options should use upstream Picard.
  - name: CollectHiSeqXPfFailMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectHsMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectIlluminaBasecallingMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectIlluminaLaneMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectIndependentReplicateMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectInsertSizeMetrics
    status: partial-native
    parity_script: tools/verify_basic_collectinsertsizemetrics_parity.sh
    native_scope: "Insert-size metrics and histograms for SAM/BAM/CRAM with REFERENCE_SEQUENCE for CRAM paths, including Picard-style second-of-pair collection, orientation-separated FR/RF/TANDEM rows, minimum-pct filtering, DEVIATIONS-based histogram trimming, lightweight PDF chart artifact, duplicate inclusion, minimum-pct alias, accumulation by sample/library/RG, and GATK NA12878 mitochondrial real-data parity."
    fallback_scope: Unsupported histogram/chart options and unsupported accumulation modes should use upstream Picard.
  - name: CollectJumpingLibraryMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectMultipleMetrics
    status: partial-native
    parity_script: tools/verify_basic_collectmultiplemetrics_parity.sh
    native_scope: "Picard default and explicit supported metric programs for SAM/BAM/CRAM with REFERENCE_SEQUENCE for CRAM paths, scoped EXTRA_ARGUMENT forwarding, and common runtime option acceptance without metrics sidecars."
    fallback_scope: Unsupported PROGRAM values and unsupported forwarded metric options should use upstream Picard.
  - name: CollectOxoGMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectQualityYieldMetrics
    status: native
    parity_script: tools/verify_basic_qualityyield_parity.sh
    native_scope: "Picard-style quality-yield metrics for SAM/BAM/CRAM with REFERENCE_SEQUENCE for CRAM paths, original-quality handling, STOP_AFTER, optional non-primary inclusion, and release-candidate real-data parity."
    fallback_scope: "No known fallback-only behavior in the current documented implementation."
  - name: CollectQualityYieldMetricsFlow
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectQualityYieldMetricsSNVQ
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectRawWgsMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectRnaSeqMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectRrbsMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectSamErrorMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectSequencingArtifactMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectTargetedPcrMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectUmiPrevalenceMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectVariantCallingMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CollectWgsMetrics
    status: partial-native
    parity_script: tools/verify_basic_collectwgsmetrics_parity.sh
    native_scope: "Common coordinate-sorted whole-genome coverage metrics for SAM/BAM/CRAM with REFERENCE_SEQUENCE, optional interval territory, explicit base-quality histogram output, STOP_AFTER, Picard-style theoretical het sensitivity sampling, and a native USE_FAST_ALGORITHM mode that defaults SAMPLE_SIZE to 0 unless that option is set explicitly. INCLUDE_BQ_HISTOGRAM defaults to false to match Picard 3.4.0 histogram output. TURBO_PICARD_WGS_FAST_DEFAULT=true applies the same SAMPLE_SIZE default when USE_FAST_ALGORITHM is omitted."
    fallback_scope: Unsupported advanced WGS options should use upstream Picard.
  - name: CollectWgsMetricsWithNonZeroCoverage
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CombineGenotypingArrayVcfs
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CompareGtcFiles
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CompareMetrics
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CompareSAMs
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: ConvertHaplotypeDatabaseToVcf
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: ConvertSequencingArtifactToOxoG
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CreateBafRegressMetricsFile
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CreateExtendedIlluminaManifest
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CreateSequenceDictionary
    status: native
    parity_script: tools/verify_basic_createdict_parity.sh
    native_scope: "Picard-style FASTA dictionary creation with MD5 sequence digests, optional file md5 sidecar, URI handling, alternate names, derived output paths, NUM_SEQUENCES limiting, gzip FASTA input, and common Picard runtime option acceptance."
    fallback_scope: "No known fallback-only behavior in the current documented implementation."
  - name: CreateVerifyIDIntensityContaminationMetricsFile
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CrosscheckFingerprints
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: CrosscheckReadGroupFingerprints
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: doctor
    status: native
    parity_script: tools/verify_basic_doctor_parity.sh
    native_scope: "turbo-picard utility command that reports local runtime state without running Picard, including version, executable path, CPU/thread policy, reference configuration, fallback resolution, PATH picard discovery, and auto-fallback state."
    fallback_scope: This is not an upstream Picard command and does not delegate to fallback.
  - name: DownsampleSam
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: EstimateLibraryComplexity
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: explain
    status: native
    parity_script: tools/verify_basic_explain_parity.sh
    native_scope: "turbo-picard utility command that explains the documented execution path for a Picard-shaped command, including native or fallback status, scope notes, resolved fallback command, declared output arguments, and schema-versioned JSON output for workflow-manager or CI integrations."
    fallback_scope: This is not an upstream Picard command and does not delegate to fallback.
  - name: ExtractFingerprint
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: ExtractIlluminaBarcodes
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: ExtractSequences
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: FastqToSam
    status: partial-native
    parity_script: tools/verify_basic_fastqtosam_parity.sh
    native_scope: "Single-end and paired FASTQ to unmapped SAM/BAM with read-group metadata, sequential FASTQ shard expansion via USE_SEQUENTIAL_FASTQS, Standard/Illumina/Solexa quality handling, automatic Standard-vs-Illumina detection, MIN_Q/MAX_Q validation, empty-line and empty-FASTQ controls, sort-order header handling, MD5 sidecars, comments, and common Picard runtime option acceptance."
    fallback_scope: "Advanced Picard-only FASTQ ingestion behavior should use fallback."
  - name: FifoBuffer
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: FilterSamReads
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: FilterVcf
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: FindMendelianViolations
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: FixMateInformation
    status: partial-native
    parity_script: tools/verify_basic_fixmateinformation_parity.sh
    native_scope: "Mate fixing for queryname-sorted one or more SAM/BAM/CRAM inputs with REFERENCE_SEQUENCE, supplementary mate updates, default output sort-order preservation, optional coordinate sorting/indexing, and MD5 sidecar."
    fallback_scope: "Non-queryname inputs and read groups without exactly two primary records should use upstream Picard."
  - name: FixVcfHeader
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: GatherBamFiles
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: GatherVcfs
    status: partial-native
    parity_script: tools/verify_basic_gathervcfs_parity.sh
    native_scope: "Concatenation of compatible VCF shards with matching samples and sequence dictionaries, common Picard runtime option acceptance, and VCF index sidecar creation when requested."
    fallback_scope: Dictionary/sample reconciliation and nontrivial VCF compatibility handling should use upstream Picard.
  - name: GenotypeConcordance
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: GtcToVcf
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: IdentifyContaminant
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: IlluminaBasecallsToFastq
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: IlluminaBasecallsToSam
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: IntervalListToBed
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: IntervalListTools
    status: partial-native
    parity_script: tools/verify_basic_intervallisttools_parity.sh
    native_scope: "CONCAT action with optional sorting, uniqueness, non-negative padding clamped to dictionary bounds, Picard-compatible negative-padding rejection, and abutting interval handling."
    fallback_scope: Set operations beyond CONCAT and scatter/count output should use upstream Picard.
  - name: LiftOverHaplotypeMap
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: LiftOverIntervalList
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: LiftoverVcf
    status: partial-native
    parity_script: tools/verify_basic_liftovervcf_parity.sh
    native_scope: "Positive-strand single-block chain liftover with reject output for simple VCF records and lifted-output VCF index sidecar creation when requested."
    fallback_scope: "Reverse-strand, gapped, multi-block, symbolic, and complex allele liftover should use upstream Picard."
  - name: MakeSitesOnlyVcf
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: MakeVcfSampleNameMap
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: MarkDuplicates
    status: partial-native
    parity_script: tools/verify_basic_picard_parity.sh
    native_scope: "SAM/BAM/CRAM duplicate marking/removal with REFERENCE_SEQUENCE, metrics, barcode grouping, optical duplicate tagging, sidecars, multi-BAM input, and release-candidate real-data parity."
    fallback_scope: Unsupported Picard MarkDuplicates options should use upstream Picard.
  - name: MarkDuplicatesWithMateCigar
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: MarkIlluminaAdapters
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: MeanQualityByCycle
    status: partial-native
    parity_script: tools/verify_basic_meanqualitybycycle_parity.sh
    native_scope: "Mean quality by cycle metrics and lightweight PDF chart artifact for SAM/BAM/CRAM with REFERENCE_SEQUENCE for CRAM paths, including reverse-strand cycle handling and original qualities."
    fallback_scope: Unsupported Picard charting and options should use fallback.
  - name: MergeBamAlignment
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: MergePedIntoVcf
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: MergeSamFiles
    status: partial-native
    parity_script: tools/verify_basic_mergesamfiles_parity.sh
    native_scope: "Repeated SAM/BAM/CRAM inputs with REFERENCE_SEQUENCE, identical dictionaries including MERGE_SEQUENCE_DICTIONARIES=true acceptance for already-compatible inputs, interval filtering for coordinate-sorted indexed inputs, RG collision rewrite, sidecars, and coordinate/queryname/unsorted output."
    fallback_scope: "True sequence-dictionary merging for non-identical dictionaries should use fallback."
  - name: MergeVcfs
    status: partial-native
    parity_script: tools/verify_basic_mergevcfs_parity.sh
    native_scope: "Merge compatible VCF inputs by dictionary order with optional explicit sequence dictionary replacement, common Picard runtime option acceptance, and VCF index sidecar creation when requested."
    fallback_scope: "Inputs with incompatible samples, missing dictionaries, or advanced merge semantics should use upstream Picard."
  - name: NonNFastaSize
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: NormalizeFasta
    status: native
    parity_script: tools/verify_basic_normalizefasta_parity.sh
    native_scope: "FASTA normalization with configurable line wrapping and Picard-compatible acceptance of common no-op runtime sidecar options."
    fallback_scope: "No known fallback-only behavior in the current documented implementation."
  - name: PositionBasedDownsampleSam
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: QualityScoreDistribution
    status: partial-native
    parity_script: tools/verify_basic_qualityscoredistribution_parity.sh
    native_scope: "Quality histogram metrics and lightweight PDF chart artifact for SAM/BAM/CRAM with REFERENCE_SEQUENCE for CRAM paths, including original-quality handling."
    fallback_scope: Unsupported Picard charting and options should use fallback.
  - name: RenameSampleInVcf
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: ReorderSam
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: ReplaceSamHeader
    status: partial-native
    parity_script: tools/verify_basic_replacesamheader_parity.sh
    native_scope: "SAM/BAM/CRAM record streaming with replacement SAM header, REFERENCE_SEQUENCE for CRAM paths, optional MD5 sidecar, SAM-compatible CREATE_INDEX handling, and common Picard runtime option acceptance."
    fallback_scope: Unsupported header/output combinations should use upstream Picard.
  - name: RevertOriginalBaseQualitiesAndAddMateCigar
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: RevertSam
    status: partial-native
    parity_script: tools/verify_basic_revertsam_parity.sh
    native_scope: "Alignment reversion for SAM/BAM/CRAM with REFERENCE_SEQUENCE, optional alignment retention, secondary/supplementary filtering, hardclip restoration, sidecars, selected attributes, and GATK NA12878 mitochondrial real-data parity."
    fallback_scope: Unsupported attribute policies and unsupported sort/order combinations should use upstream Picard.
  - name: SamFormatConverter
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: SamToFastq
    status: partial-native
    parity_script: tools/verify_basic_samtofastq_parity.sh
    native_scope: "Single-end, paired, dedicated unpaired FASTQ, interleaved, gzipped, per-read-group OUTPUT_PER_RG output with PU/ID routing and OUTPUT_DIR support, and MD5 FASTQ output from SAM/BAM/CRAM with REFERENCE_SEQUENCE, Picard-compatible RE_REVERSE handling, primary/PF filtering, clipping-attribute actions, read-end trimming, quality end-trimming, max-bases output caps, common Picard runtime option acceptance, and GATK NA12878 mitochondrial real-data parity."
    fallback_scope: Unsupported Picard FASTQ export combinations should use upstream Picard.
  - name: SamToFastqWithTags
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: ScatterIntervalsByNs
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: SetNmAndUqTags
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: SetNmMdAndUqTags
    status: partial-native
    parity_script: tools/verify_basic_setnmmdanduqtags_parity.sh
    native_scope: "Coordinate-sorted SAM/BAM/CRAM NM, MD, and UQ tag calculation against a FASTA reference with REFERENCE_SEQUENCE for CRAM paths, MD5 sidecar, and common runtime option handling."
    fallback_scope: "Bisulfite mode, CIGAR ref-skip handling, and unsupported reference/tag options should use upstream Picard."
  - name: SimpleMarkDuplicatesWithMateCigar
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: SortGff
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: SortSam
    status: partial-native
    parity_script: tools/verify_basic_sortsam_parity.sh
    native_scope: "Coordinate and queryname sorting for SAM/BAM/CRAM with REFERENCE_SEQUENCE, sidecars, streaming fast path for already-sorted inputs, and GATK NA12878 mitochondrial real-data parity."
    fallback_scope: Unsupported sort orders and advanced Picard sorting options should use fallback.
  - name: SortVcf
    status: partial-native
    parity_script: tools/verify_basic_sortvcf_parity.sh
    native_scope: "Sort compatible VCF inputs by sequence dictionary order with optional explicit dictionary replacement, common Picard runtime option acceptance, and VCF index sidecar creation when requested."
    fallback_scope: "Inputs with incompatible samples, missing dictionaries, or advanced VCF normalization should use upstream Picard."
  - name: SplitSamByLibrary
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: SplitSamByNumberOfReads
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: SplitVcfs
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: UmiAwareMarkDuplicatesWithMateCigar
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: UpdateVcfSequenceDictionary
    status: partial-native
    parity_script: tools/verify_basic_updatevcfsequencedictionary_parity.sh
    native_scope: "Replace VCF contig headers from a Picard sequence dictionary while preserving stable records, accepting common Picard runtime options, and writing a VCF index sidecar when requested."
    fallback_scope: Unsupported VCF header forms and advanced dictionary reconciliation should use fallback.
  - name: ValidateSamFile
    status: partial-native
    parity_script: tools/verify_basic_validatesamfile_parity.sh
    native_scope: "SUMMARY and VERBOSE validation for SAM/BAM/CRAM with REFERENCE_SEQUENCE for CRAM paths, supported mate, missing-mate, read-group, missing-platform, record, unmapped-MAPQ, and warning issue types with IGNORE filtering, SKIP_MATE_VALIDATION handling, common runtime option acceptance, and GATK NA12878 mitochondrial real-data parity for summary histogram plus exit code."
    fallback_scope: "Unsupported validation modes, IGNORE values, and full Picard validator issue coverage should use upstream Picard."
  - name: VcfFormatConverter
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: VcfToAdpc
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: VcfToIntervalList
    status: fallback-only
    native_scope: "Delegated to upstream Picard 3.4.0. turbo-picard runs the native accelerated implementation when one exists; otherwise it transparently forwards to upstream Picard when fallback is configured or auto-discovered."
    fallback_scope: Transparent upstream Picard 3.4.0 delegation. No native fast path yet.
  - name: ViewSam
    status: partial-native
    parity_script: tools/verify_basic_viewsam_parity.sh
    native_scope: "Picard-compatible SAM/BAM/CRAM viewing to stdout with REFERENCE_SEQUENCE, header-only, records-only, interval-list, Aligned/Unaligned alignment-status filters, PF/NonPF status filters, and release-candidate real-data parity. turbo-picard also accepts OUTPUT as a convenience extension for file output."
    fallback_scope: "Unsupported filter combinations and any workflow that needs strict upstream ViewSam argument-surface matching should use upstream Picard."