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
  • Postprocessing variant calls
    • vardict_filter_case-control 0.1.5
    • vardict_filter_single-sample 0.1.5
    • maf_annotated_by_bed_0.2.2
    • maf_annotated_by_tsv_0.2.3
    • maf_filter_cmoch_0.2.3
    • maf_tag_cmoch_0.2.3
    • maf_annotated_by_bed_0.2.3
  • sequence_qc
  • SnpSift
  • Trim Galore
  • Ubuntu utilites
  • VarDictJava
  • VCF2MAF
  • Waltz
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Postprocessing variant calls

vardict_filter_case-control 0.1.5vardict_filter_single-sample 0.1.5maf_annotated_by_bed_0.2.2maf_annotated_by_tsv_0.2.3maf_filter_cmoch_0.2.3maf_tag_cmoch_0.2.3maf_annotated_by_bed_0.2.3
PreviousMarkDuplicates v4.1.8.1Nextvardict_filter_case-control 0.1.5

Last updated 3 years ago