CIGAR M operator maps off end of reference

Question

[Chirag Nepal]

Hi,

I am trying to mark duplicates using Picardtool, and i get this error:

Exception in thread "main" net.sf.samtools.SAMFormatException: SAM validation error: ERROR: Read name HWI-ST165_314:5:1206:2882:164986, CIGAR M operator maps off end of reference

I would like to throw/trim those few reads which map across the end of reference coordinates. Any suggestions.

Answer 1

[smilefreak]

Picard's CleanSam should do the job.