Help with GATK WDL for somatic snp

0

Hi, I'm trying to use the WDL from GATK for somatic SNV.
github.com/gatk-workflows/gatk4-somatic-snvs-indels

I ran this locally with the provided example and seem to work fine no errors, however according to the readme it states:

Outputs
unfiltered vcf
unfiltered vcf index
filtered vcf
filtered vcf index

When I run this locally it produces an output subfolder "call-M2" in here there are 49 subfolders labeled as "shard-X" X= 1 to 49. Each one of these folders there is an output.vcf and index. There are no other documentations. So I'm very confused. What are each of these "shard" folder? And how do I do get so that there is a single VCF filtered file?

thanks!
A


gatk


snv

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