to claculte % deletion and insertion after mapping.

[vishwesh]

Hi,
I want to measure the % of insertion and deletion in mapping to reference genome. I was using BWA for mapping and I get a .bam file. Is there any way I could do this??

Regards
Vishwesh

[blaboon]

I think the CIGAR string can help you. Because the CIGAR can tell you how many insertions and deletions in your mapping for each read, then you can sum them up and divided by the total number of bases you have (maybe you can use the sum of CIGAR length for all reads).

For details of CIGAR, you can check the SAM specification document

[Brian Bushnell]

If you map with BBMap, it automatically generates a summary of the percent of reads and bases that had insertions and deletions. It also produces, if you set "indelhist=indelhist.txt", a file containing the exact number of insertions and deletions of specific lengths. I strongly recommend BBMap if you are specifically interested in indels, as it is much more sensitive to indels (particularly long ones) than other aligners.