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Find deleted regions from WGS data/ IGV viewer?

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!

next-gen assembly

1 answer

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

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