If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: GATK-188.8.131.52
b) Exact command used: Followed this post workflow (https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants)
c) Entire error log:
I followed the above link Germline CNV calling workflow for our cohort samples. I am having a few doubts about the results. The below are my question:
1. In the output .vcf file, why only one sample name was reported for the INFO column of the header (attached screenshot)? Usually,population-level variant calling results have to provide each sample independently?
2. How to calculate allele frequencies for our cohort result?
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