Can you please provide
a) GATK version used: GATK 126.96.36.199
b) Exact GATK commands used N/A
c) The entire error log if applicable. N/A
Hello! I am attempting to implement the GATK 188.8.131.52 "best practices pipelines" for (1) Data Pre-processing for Variant Discovery, (2) Somatic short variant discovery (SNVs + Indels), and (3) Somatic Copy Number Variant Discovery on human WES and WGS data.
I downloaded the most recent version of the hg38 resource bundle from here:
I have two overarching questions that I could not find in the manual documentation:
1. What are the differences and origins of the various known variation vcf files in the hg38 resource bundle? I see the following vcf files downloaded from the site:
2. For the "best practices" pipelines for (1) Data Pre-processing for Variant Discovery, (2) Somatic short variant discovery (SNVs + Indels), and (3) Somatic Copy Number Variant Discovery on human WES and WGS data, which vcf files should I use at the various steps requiring known variants?
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