get deletion coverage from .bam file

Question

[biositemap55]

Dear all:

I mapped the NGS whole genome sequencing reads to reference genome sequence, to detection natural variations of CDS region. To filter out some protein coding genes might with negative deletion calling, I want to get the coverage of every deletion variation. Like if there there are 5 reads go cross an deletion, I expect the depth would be 5.

I tried "samtools depth", but it would not give the expected result. If all the reads confirm a deletion, the samtools would output the depth as 0.

Any idea to do that please?

Answer 1

[Brian Bushnell]

BBMap's pileup.sh program by default considers deletions as covered. This can be turned on or off.

Answer 2

[trausch]

bedtools coverage -abam <align.bam> -b <deletion.bed>