Hi Mark, It would be helpful if you showed the exact command used and also how you confirmed that an alignment was lost. Just this week I saw a post (elsewhere) where someone was losing reads in converting from SAM->BAM only to find that it was due to misusing an obscure (present but undocumented in version 0.1.19) option.
Best, Devon ____________________________________________ Devon Ryan, Ph.D. Email: dpr...@dpryan.com Tel: +49 (0)178 298-6067 Molecular and Cellular Cognition Lab German Centre for Neurodegenerative Diseases (DZNE) Ludwig-Erhard-Allee 2 53175 Bonn, Germany On Aug 29, 2014, at 12:10 AM, Mark Wadsworth wrote: > Hello, > > We have been comparing whole genome sequence bam files and we have found that > samtools sort -n either removes or modifies the reads as it sorts. We have > tried it on both the older version and version 1.0 and have had the same > results. We found that several reads are in our original file, but after > sorting they are no longer there. I am not sure as to what could be causing > this. We have checked to make sure that we are running the program as > specified in the specs. We have not gone into the source code to try and > identify the problem. We have run it several times with consistent results. > Any help or advice is welcomed. > > Thanks, > Mark > ------------------------------------------------------------------------------ > Slashdot TV. > Video for Nerds. Stuff that matters. > http://tv.slashdot.org/_______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
