Hi all, I'm looking for a tool or PERL module that could take each line from a SAM file and parse the CIGAR + MD strings to output the genomic coordinates of all mismatches (specifically SNPs). I know of multiple tools that will tally up the number and type of mismatches at each position in a genome, but what I need is the reference position of all SNPs within each pair of mates in my SAM files.
I can write a PERL script to do this, but I'm hoping that I'm not the first person to encounter this issue!
Thanks,
Carlo
I can write a PERL script to do this, but I'm hoping that I'm not the first person to encounter this issue!
Thanks,
Carlo
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