Dear all,
I'm a software engineer at bioinformatics startup and we’ve been using
Samtools Mpileup for our variant calling pipeline. We've been working to
distribute the variant calling computation by using the '-r' option to
`split` the genome into smaller regions, and run mpileup on each one
separately, in parallel. We are recently using Samtools 1.1 and notice
discrepancies in the results, between running `without splitting` and `with
splitting`. Although most variants are consistent, there are small
differences in the called variants and the quality scores. For example, in
an analysis of a single exome sample, mapped using BWA men, a SNP is found
in a run with splitting, but not found in a run without splitting.
Furthermore, this SNP is located far away from the split boundaries.
There is already a relevant question asked before, but with no answer thus
far: http://sourceforge.net/p/samtools/mailman/message/30802728/. We are
aware about the relevant FAQ at
https://github.com/samtools/samtools/wiki/FAQ, which attributes major
differences (between specifying a region VS without) in the samtools prior
to V0.1.17, to the BAQ calculation. However, as this thread
http://sourceforge.net/p/samtools/mailman/message/30802728/ also pointed
out, we're still seeing differences (although much fewer) with the more
recent versions of samtools.
Does anyone else face similar difficulty? We’d appreciate your help/
direction regarding the reason for this discrepancy and how we should
handle this.
Kind regards
-Kevin
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