Depth of Coverage
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Entering edit mode
16 months ago

Hello

I am dealing with the whole exome data, and want to filter out the variants whose depth of coverage for alt divided to ref allele (alt/ref) is less than or equal to 30%.

This is what the .tsv file looks like:

chr1    45797228        45797228        C       T       PASS    het   68      13.77   60.00   99   68      944,0,1119      **37,31**    1       exonic ...............................

Column 14 ("37,31") is the column of my interest.

37: depth of coverage for ref allele, 
31: depth of coverage for alt allele

Would you please help me with how to do that? I'm working with Linux, and need something like an awk command.

Data Coverage WES Filtering • 387 views
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