issue #195: Implement new mutect2 variant calling strategy

epam / fonda

Fonda is a framework which offers scalable and automatic analysis of multiple NGS sequencing data types

Apache License 2.0

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issue #195: Implement new mutect2 variant calling strategy #207

Closed kamyshova closed 3 years ago

kamyshova commented 3 years ago

Resolves #195 The pull request provides implementation of the new gatk4 mutect2 variant calling strategy:

Added new templates after mutect2 tool:
- GetPileupSummaries
- CalculateContamination
- LearnReadOrientation
- SortBamout
- FilterMutectCalls
- FilterAlignmentArtifacts
Realignment was skipped for gatk4 mutect2

syansanofi commented 3 years ago

@kamyshova Different issues: I am getting -normal NA when using tumor only.
Vardict & strelka2 all run without matching control with "NA" set as control.

kamyshova commented 3 years ago

@syansanofi Fixed