Find deleted regions from WGS data/ IGV viewer?

Question

[Clarence Yeung]

This might be a naive question, but is there a way to determine which regions of the genome didn't get any reads from WGS data? I'm working S. cerevisiae data and instead of going to each locus and manually checking each delete (ie. ura3∆ his3∆), is there a simpler solution? Thanks!

Answer 1

[Pierre Lindenbaum]

samtools depth -aa in.bam | awk '($3==0)'

[Clarence Yeung]

Works great, thanks a lot!

[Pierre Lindenbaum]

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