I am using the snakemake pipeline to analyse pairs of cancer-control samples of WES data.
I got some error and then I realize that the cause of the error is that the countPysam script returns 0 counts for all entries in both ref and alt nucleotides, no matter how low the quality filters are.
I think the problem is that this for loop is never used
for p in _p:
print(p.pos)
if p.reference_pos == position:
for r in p.pileups:
if not r.is_del and not r.is_refskip:
base = r.alignment.query_sequence[r.query_position-1]
mapq = r.alignment.mapping_quality
baseq = r.alignment.query_qualities[r.query_position-1]
if mapq >= map_quality and baseq >= base_quality:
bases.append(base)
I am using the snakemake pipeline to analyse pairs of cancer-control samples of WES data. I got some error and then I realize that the cause of the error is that the countPysam script returns 0 counts for all entries in both ref and alt nucleotides, no matter how low the quality filters are. I think the problem is that this for loop is never used for p in _p: print(p.pos) if p.reference_pos == position: for r in p.pileups: if not r.is_del and not r.is_refskip: base = r.alignment.query_sequence[r.query_position-1] mapq = r.alignment.mapping_quality baseq = r.alignment.query_qualities[r.query_position-1] if mapq >= map_quality and baseq >= base_quality: bases.append(base)
Did anyone had this problem?