Hi, I am new to exome-seq and would be grateful for any suggestions :)
I want to check coverage for variants called with MuTect2 (GATK 188.8.131.52).
I would like to filter variants basing on the number of reads at the given position and the number of reads in which alternate alleles have been called.
However, I am not sure which annotation should I analyze. I found "AS_SB_TABLE" annotation, and I am wondering - does it show total read counts for reference and alternate alleles? Or are the reads number somehow normalized for the strand bias tests?
Here is the header for "AS_SB_TABLE":
##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for **strand bias tests**. Includes the reference and alleles separated by |.">