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Calculating coverage from ref and alt columns?

Forgive this beginner question...I'm a bit new to this.

I have what looks like a vcf file with some of the headers as: chr, pos, ref, alt, etc

I was asked to find the coverage by adding the ref and alt and finding the maximum value. But since the ref and alt columns aren't numeric, what do I add?

A table example is: 

chr  ref    alt
7     G      A
7     G      A
7     G      A
7     A      G
7     A      G
7    GA      G

Do I count the number of occurences of lets say 'G' in the ref column...and then add them to the number of occurrences of 'G' in the alt column?

coverage
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written by PsFeathers • PsFeathers
  1. Its not a vcf looking like file. you do not have SNP position.
  2. Do you want to find the coverage of ref and alt base from a BAM file ?
• 1 views • link
written by GouthamAtla GouthamAtla

Sorry I am new to bioinformatics too... I have problem on getting mean coverage, I've tried 'bedtools coverage' and 'samtools pileup', but the outputs are per site or region. I was wondering how can I get just one value (say 70X) averaged depth for CDS regions.

• 0 views • link
written by jjaimi921129 • jjaimi921129

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