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Fully parameterized example workflow for somatic variant calling

dannykwellsdannykwells San FranciscoMember ✭✭

Hi again GATK folks,

Ya'll provide a lot of nice resources to get up and going with GATK, but what I can't find for the life of me is information on a functioning somatic variant calling pipeline where the functions used - from preprocessing up through calling variants - are parameterized. I've found lots of figures like this:
https://software.broadinstitute.org/gatk/img/BP_somatic_workflow_mutect1.png
but each node there a) represents several function calls! and b) does not give ANY information about the MANY parameters and options that it could be called with! So like, it's pretty hard to build your own pipeline just from this figure (and even watching the workshop videos hasn't helped much). It it would be great if there was a set of options from Broad like "this usually works and is a good place to start for parameters" for each function called (that aren't just defaults...)

EVEN better, it would be AMAZING if anyone could share with me an existing, comprehensive WDL script for calling somatic variants - like this (https://software.broadinstitute.org/wdl/userguide/topic?name=wdl-scripts) but covering the steps from fastq/unaligned bam to mutect called variants.

Thanks!!

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