Hi there,
Looks like samtools mpileup format does not out put discordant information
hidden by the soft-clipped read segments.
Often times this could be mis leading in calculating actual allele frequecy
percentages, especially when you are looking at multi base pair deletions.
In one of the cases I have seen today, I have 1300 reads supporting the 30
base pair deletion, but the aligner some how soft clipped the reads (which
are 97% of them ) and left long reads with deletions intact (no soft
clipping ) in the bam file.
so when I run the mpileup through, I get about 27 reads supporting the
deletion and rest of them are being ignored.
My question to you , is there a way to deal with such instances within
mpileup format itself than to look at CIGAR signatures on a case by case
basis?
Thanks,
Aparna
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