Command Line Tools (CWL)
Ctrlk
  • MSK-ACCESS command-line tools
  • ABRA2
  • access_utils
  • bcftools
  • Bedtools
  • Biometrics
  • Delly
  • Disambiguate
  • Fastp
  • Fgbio
  • GATK
  • GetBaseCountsMultiSample
  • Manta
  • Marianas
  • MultiQC
  • MuTect
  • Merge Fastq
  • Mosdepth
  • Octopus
  • Oncokb_annotator
  • Picard Tools
    • AddOrReplaceReadGroups v1.96
    • AddOrReplaceReadGroups v2.21.2
    • AddOrReplaceReadGroups v4.1.8.1
    • CollectAlignmentSummaryMetrics v2.8.1
    • CollectAlignmentSummaryMetrics v2.21.2
    • CollectMultipleMetrics v2.8.1
    • CollectMultipleMetrics v2.21.2
    • FixMateInformation v1.96
    • FixMateInformation v2.21.2
    • FixMateInformation v4.1.8.1
    • HSmetrics v2.8.1
    • HSmetrics v2.21.2
    • MarkDuplicates v1.96
    • MarkDuplicates v2.8.1
    • MarkDuplicates v2.21.2
    • MarkDuplicates v4.1.8.1
  • Postprocessing variant calls
  • sequence_qc
  • SnpSift
  • Trim Galore
  • Ubuntu utilites
  • VarDictJava
  • VCF2MAF
  • Waltz
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Picard Tools

AddOrReplaceReadGroups v1.96AddOrReplaceReadGroups v2.21.2AddOrReplaceReadGroups v4.1.8.1CollectAlignmentSummaryMetrics v2.8.1CollectAlignmentSummaryMetrics v2.21.2CollectMultipleMetrics v2.8.1CollectMultipleMetrics v2.21.2FixMateInformation v1.96FixMateInformation v2.21.2FixMateInformation v4.1.8.1HSmetrics v2.8.1HSmetrics v2.21.2MarkDuplicates v1.96MarkDuplicates v2.8.1MarkDuplicates v2.21.2MarkDuplicates v4.1.8.1
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Last updated 3 years ago