Hi Alison, mpileup ignores reads with the flags UNMAP,SECONDARY,QCFAIL,DUP. The status of the mate is not checked by default.
Best wishes, Petr On Wed, 2015-11-18 at 10:36 +0000, Wright, Alison wrote: > I wish to call SNPs using SAMtools mpileup function. > > I first map my Illumina paired end reads to the reference using Bowtie > and then I have custom scripts that filter out non-uniquely mapping > reads. To do this I rely on the absence of XS to indicate a uniquely > mapped read. > > > > However, this creates a potential problem as the SAM flags are often > no longer meaningful. > > Eg. Originally I have two reads that are paired and both map > > Forward read flag 83 > > Reverse read flag 163 > > If Forward read is not uniquely mapping then I remove this from the > sam file, leaving Reverse read intact. The flag of Reverse read is not > changed and therefore now falsely indicates it has a mapped pair. This > isn’t a problem if my downstream programs do not use the flag. > > > > Therefore, I wanted to check, does the mpileup function read/use the > flags in the sam file? > > > > If so, is there another way to only use uniquely mapping reads to call > SNPs. > > > > Thanks very much > > > ------------------------------------------------------------------------------ > _______________________________________________ > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
