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
sequence_qc
SnpSift
Trim Galore
Ubuntu utilites
VarDictJava
VCF2MAF
Waltz

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GATK

ApplyBQSR v4.1.2.0 ApplyBQSR v4.1.8.1 BaseRecalibrator v4.1.2.0 BaseRecalibrator v4.1.8.1 MergeBamAlignment v4.1.8.0 MergeSamFiles v4.1.8.0 SamToFastq v4.1.8.0

Previoussimplex_filter v0.1.8 NextApplyBQSR v4.1.2.0

Last updated 3 years ago