CIGAR M operator maps off end of reference
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.
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Chirag Nepal
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Chirag Nepal
1 answer
Picard's CleanSam should do the job.
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