Hi

Can we sort BAM files according to the read name? As the normal sorting happens on the co-ordinates, can anyone tell how to sort a BAM file on read names? I am trying to run HT-Seq count on paired end SAM files but receiving warnings  for which I have to sort the BAM in read names and then create its SAM and then run HT-Seq
See Picard's SortSam command below. You can sort a sam or bam file using queryname or readname.

http://picard.sourceforge.net/command-line-overview.shtml#SortSam