MuTect2 annotations: number of reads at the given position

Question

[wiki97]

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 4.1.8.1).

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?

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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 |.">

Answer 1

[Pierre Lindenbaum]

number of reads at the given position

look at FORMAT/DP (or INFO/DP)

number of reads in which alternate alleles have been called.

see FORMAT/AD

[wiki97]

Dear Pierre Lindenbaum, thank you very much for your answer!!