Email for v7. Bug found that printed G’s as C’s and vise versa.
Call SNPs from sam files in a method similar to Hohenlohe et al 2010. Updated to v4 Feb 9. Previous version had a bug.
It is now fixed up for all of BWAs cigars flavors.
This only deals with reads that fit one of the following:
Full alignment (55M)
Soft clip at the start (10S45M)
Soft clip at end (45M10S)
One deletion (25M10D25M)
One insertion (20M10I20M)
This means it ignores reads with a cigar fields that have N, H, P, = or X and it ignores reads with a cigar more complicate then a single soft clip or a single indel. It also does not penalize reads adjacent to indels.
It ignores bases in soft clipped parts of reads