Picard Error with SAM File
Hi
I'm new in bioinformatics. I was trying to add Read Group to a SAM file by Picard and I got this error:
{Exception in thread "main" htsjdk.samtools.SAMFormatException: Error parsing text SAM file. MRNM not specified but flags indicate mate mapped; File /home/masoud/NGS/Samples/54992.sam; Line 744
Line: MISEQ:131:000000000-A565J:1:1101:12427:6217 65 chr13 32904990 219 214M36S * 0 0 GGGGACTACTACTGTATGTGCATTGAGAGTTTTTATACTAGTGATTTTAAACTATAATTTTTGCAGAATGTGAAAAGCTATTTTTCCAATCATGATGAAGGTCTGAAGAAAAATGATAGATTTATCGCTTCTGTGACAGACAGTGAAAACACAAATCAAAGAGAAGCTGCAAGTCATGGTAAGTCCTCTGTTTAGTTGAACTACAGGTTTTTTTTTGTTGTTGTTTTGCTTTTTTTTTTTTTTGATGTGG 1AAAADCCFFFFGGG3FGGDFAGHBHHGH1FGHGHHHHHGCDDGHGHHGAEGHHHHHHHHHHGGHHFEGHHG22DAAGHHHFHHHHHHGHHHHH2GHHDFFGHHFHHGFHHGHFHHHHHHHHHHHHHGHHGHHHHHHHHHHHHHHF>GHHFGHFGHHHFFHHHGHHHGHHGFHGDDG>GF2FGGGHHHHGHHHGHHF1F1?GHFFGFHDGGGGGGGCHHFHHHCGHHG0;CFHHGGGGG@@@?####### AS:i:206 XS:i:0 XF:i:0 XE:i:5 NM:i:2}
What is this? What should I do to solve it?
Thank you
Masoud
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This is one of the known discrepancies between the SAMtools specification and Picard's validation of the format: see http://sourceforge.net/p/samtools/mailman/samtools-devel/thread/AB0E0502-911B-444C-B112-AA9248C7AA00@sanger.ac.uk/
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How did you create that SAM file? Whichever aligner you used has a bug. I or someone else here could write a little python program to get around this particular error, but I worry about the validity of the alignments in general if the output is broken like this.
Hi,
Please use appropriate tags when you create posts. You'd used "forum" (which is not relevant here), and I changed it to "sam" and "picard". The system is designed to alert people subscribed to certain tags when new posts are created with those tags, so you stand a better chance of getting faster responses if you use the right tags.