I am new to biostar so I want start by saying thank you all for sharing your expertise.
I recently started testing stampy-1.0.21. I align with bwa-0.5.9-r16 and use output redirection to pipe bwa sam output into stampy to align the bwa output. I use standard options for both tools with --bamkeepgoodreads for stampy. The issue I have is the BWA mapped reads and stampy mapped reads have differently scaled (so it seems) read mapping qualities. bwa mapq max is 60 and stampy mapq max is 99. For instance reads that where aligned initially with bwa with poor mapping quality scores, stampy aligns them much better (there is a large indel) but the mapq is 99 now. This arises as an issue during variant calling especially for reads aligned with stampy with more mismatches (like mapq 70 out of 99) than the bwa aligned reads (mapq 60). The result is higher false-positives with mpileup | bcftools even though mpileup has max mapq at 60 by default. if mpileup rescales mapq it should not be a problem however, it seems so not scale but limit at 60. One thing I have realized is the differences in bwa and stampy defaults for substitution rates.
Has anybody else seen this problem, or what am I doing wrong. Thanks.