How to correct SAM file for the errors reported by PICARD ValidateSAMFile ?

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Samantha Marie Waters

the errors are pretty straight forward. invalid mapping quality of read 21 means it falls below or above the cutoff value in the parameters. mate not found means that the pair-end read for 730 was not in your sequences. mismatch mate means those reads aren't paired properly.

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

http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page#Q:_MarkDuplicates_.28or_ValidateSamFile.29_produces_the_error_.22Value_was_put_into_PairInfoMap_more_than_once..22__What_should_I_do.3F

Sourav Nayak

Thanks Samantha. I understood the meaning of these errors. I want to understand these situation more elaborately. Why these error situations came into picture? As per my inspection, data provided to me is perfectly paired. So is it possible that BWA (ver-5.9rc1) is unable to find pair for some reads !!!! Is it a bug??? Anyways I will try newer versions of BWA to get an idea.

As you mentioned about MergeBamAlignment, it is really not clear to me how merging of mapped.bam with unmapped.bam can help this thing out. Even if I separate reads having errors using script, does meging it back with reads without errors can serve me the purpose.

Looking forward to more inputs...

Christian Cole

This has been addressed on the samtools mailing list:

http://sourceforge.net/mailarchive/forum.php?thread_name=3139BD46-2BD9-4B6A-9B50-C3039BA9AD37%40broadinstitute.org&forum_name=samtools-help

Thanks Christian. Actually the thread was created by me in SAMTools Mailing list. There Alec showed me the way resolve those. Right now I am exploring the reasons for such discrepencies in SAM files after BWA alignment. Any inputs regarding the errors is highly appreciated.

Thanks again.