How to get Allele Coverage from bam file or vcf file?

Question

[murali]

I am working with targeted sequencing, I want to find the allele coverage?

What is the allele coverage, and how can I extract it from bam or vcf file?

(If I understood correct, for particular allele how many number of reads mapped) Is that correct?

[Sandeep]

How are you calling the variants? I mean samtools, GATK, varscan etc.

Answer 1

[Ram]

The term you're looking for is Allele Depth. It can be found in the INFO field for every sample. Google Allele Depth + <target_operation> (calculate, filter, etc) and you will see tools to get your target operation done.

This (4 year old) thread suggests a possible catch to this though - Sum(AD) need not be equal to DP. Not sure if this applies today, and to all variant callers.

Search the forum for Allele Depth - there's plenty of stuff in here.