Hi Aparna, no, sorry. Samtools relies on the aligner to determine the soft clipping correctly. Maybe you could try with a different aligner or edit the cigars with a dedicated program/script of yours.
petr On Tue, 2014-09-09 at 15:08 -0400, Aparna wrote: > 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 > > > > > > ------------------------------------------------------------------------------ > Want excitement? > Manually upgrade your production database. > When you want reliability, choose Perforce. > Perforce version control. Predictably reliable. > http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk > _______________________________________________ > 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. ------------------------------------------------------------------------------ Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
