Hello Ryan, On Tue, Feb 16, 2016 at 11:22:18PM +0000, Friedman, Ryan wrote: > samtools view -S -b foo.sam > foo.bamnorg # convert from sam to bam > bamaddrg -b foo.bamnorg > foo.bam # ensure read groups are attached > samtools sort foo.bam foo.sorted .bam # sorts > samtools index foo.sorted.bam # index the sorted bam > samtools rmdup foo.sorted.bam foo.sorted.1.bam # remove duplicate reads > freebayes ... > > The entire pipeline works fine up until rmdup where it immediately results in > a segmentation fault.
I have a fix for this now at https://github.com/samtools/samtools/pull/539 It's tiny so you can just manually insert the 2 additional lines in samtools/bam.c to your local copy and recompile, if you don't want to deal with using git. (Click on "files changed" to see the edit.) Rmdup no longer crashes, although I haven't tested the validity of its results. Maybe you should consider adding LB tags to your read group headers anyway as without them rmdup considers all the read-groups to be within the same library. Thanks for reporting the issue. James -- James Bonfield ([email protected]) | Hora aderat briligi. Nunc et Slythia Tova | Plurima gyrabant gymbolitare vabo; A Staden Package developer: | Et Borogovorum mimzebant undique formae, https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi. -- 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. ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
