Command Line Tools (CWL)

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develop

MSK-ACCESS command-line tools
ABRA2
- v2.17
- v2.22
access_utils
- 0.1.1
bcftools
Bedtools
Biometrics
Delly
- delly call 0.9.1
- delly call 1.0.3
Disambiguate
- v1.0.0
Fgbio
GATK
GetBaseCountsMultiSample
- 1.2.5
Manta
- Manta v1.5.1
Marianas
MultiQC
- MultiQC v1.10.1.7
- MultiQC v1.12
MuTect
- MuTect 1.1.5
Merge Fastq
- v0.1.7
Mosdepth
- 0.3.3
Octopus
- v0.7.4
Oncokb_annotator
- v3.2.2
Picard Tools
Postprocessing variant calls
sequence_qc
- v0.2.4
SnpSift
- v5.0
Trim Galore
- v0.6.2
Ubuntu utilites
- v18.04
VarDictJava
- v1.8.2
VCF2MAF
- 1.6.21
Waltz
- CountReads v3.1.1
- PileupMetrics v3.1.1

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