Bam Output Mismatch By Contig

[crkessen]

I've been looking for something that extracts the %mismatch by contig from a .bam file. (Not unlike the left navigation panel in Tablet does automatically.)

Unfortunately I have been unable to find anything. I can't imagine I'm the first person who has wanted this information.

Does anyone have any ideas/solutions to this problem?

Id rather not try to reinvent the wheel.

[westerman]

I am unfamiliar with Tablet's display so I may be totally off-base. I presume you are talking about SNPs and not InDels. I am unaware of a program that does what you want. In general depends on where your BAM file came from. Assuming that you already have the comparison then you could look at the CIGAR string and count up the number of mismatches if the program puts those in (character 'X'). However this may take a (simple) custom program. Usually what I do is to use samtools 'mpileup' option piped through bcftools in order to create a VCF file that is summarized. Once again some programming is required to extract information from the VCF file.

[crkessen]

Thanks for your reply. It looks like that is what I'm going to have to do!