Hi,
I noticed that WASP does not handle correctly the D and I entries in CIGAR. That leads to incorrectly identify the nucleotide overlapping a SNP. Thus leading to an erroneous number of reads per allele.
The problem arises because when a D or I is encountered, WASP does not update the genomic start index (when D) or the read start index (when I) and therefore causing an unwanted shift between read and genome.
Hi, I noticed that WASP does not handle correctly the D and I entries in CIGAR. That leads to incorrectly identify the nucleotide overlapping a SNP. Thus leading to an erroneous number of reads per allele.
The problem arises because when a D or I is encountered, WASP does not update the genomic start index (when D) or the read start index (when I) and therefore causing an unwanted shift between read and genome.
I implemented a fix for this.
Thanks, Mingshi