Hi Marc, thank you for providing an example. This indeed looks like a limitation of samtools, it does not handle correctly indels like "5D0M6I". I'll take a look and see if it can be improved.
Cheers, Petr On Tue, 2014-10-21 at 14:34 +0200, Marc Sturm wrote: > Hi all, > > we use samtools for variant calling and the results always looked > good. > Now, we noticed that samtools 1.1 misses a pretty clear indel in one > of our samples. > > It is a 6-base deletion combined with a 7-base insertion, which in sum > leads to a frameshift. > The 151pb paired-end reads were produced on an Illumina MiSeq. > Haloplex enrichment was used for the library preparation > (amplicon-based). > > The BAM file and Makefile with the commands and parameters can be > downloaded here: > https://docs.google.com/uc?export=download&id=0B-iHdfk93LueVGQ2bTVUMTJSZVE > > Other callers, like FreeBayes and GATK HC can call the variant. > Is this a bug in samtools? Or do we need to set special parameters to > call this variant? > > Thanks, > Marc > > > ------------------------------------------------------------------------------ > Comprehensive Server Monitoring with Site24x7. > Monitor 10 servers for $9/Month. > Get alerted through email, SMS, voice calls or mobile push notifications. > Take corrective actions from your mobile device. > http://p.sf.net/sfu/Zoho > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > 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 Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
