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
