Hi Amy, You could try novosort -n, it doesn't do any validation, just sorting. You can download as part of novocraft suite from www.novocraft.com. Without a license it will run single threaded so I've attached a tar with a license file that will enable threading. Just extract the file novoalign.lic and save into the same folder as novosort.
novosort -n --tmpdir . --ram 4G input.bam >output.bam Kind Regards, Colin On 16 October 2014 03:12, Amy Williams <alw...@cornell.edu> wrote: > All, > > I've got several .bam files that Illumina generated, aligned using their > aligner (Eland2?). I want to redo the alignments with BWA MEM and so > need fastq files. To get fastqs, I first need to sort on read name. > > This is going smoothly for most of the .bams, but I've encountered a few > issues. > > 1. For some .bams, both samtools sort -n and Picard's SortSam crash. > Picard issues an error "Read CIGAR M operator maps off end of > reference". If I must lose reads that map off the end of the sequence, > that's fine, but a serious issue here is that the resulting sorted .bam > file has fewer reads than the original. Since the alignment itself > doesn't matter to me, is there a way to change these reads to be > unmapped? Or just drop them? I don't want to lose other good data. > > 2. In a few other cases, samtools sort produces truncated files with no > error message. Should I double check read counts each time I sort? > > > -Amy > > > ------------------------------------------------------------------------------ > 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 >
TrialLicense.tar.gz
Description: GNU Zip compressed data
------------------------------------------------------------------------------ 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
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