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Old 06-05-2012, 08:16 AM   #1
Location: Iowa

Join Date: Aug 2010
Posts: 23
Default Picard Issue

I am having an issue with a BAM file in picard. I tried to run AddOrReplaceReadGroups on the file and got the following error, and this is with VALIDATION_STRINGENCY=SILENT:

Exception in thread "main" net.sf.samtools.SAMFormatException: For sequence 0, text and binary have different lengths in file

When I tried to run ValidateSamFile, I get the same error. What is wrong with my BAM file that it would be giving me this error, especially with VALIDATION_STRINGENCY=SILENT? Thanks.
ercfrtz is offline   Reply With Quote
Old 06-05-2012, 09:00 AM   #2
Location: USA

Join Date: Mar 2012
Posts: 21

Just taking a blind guess from what you posted, it looks like the bam file and the index do not match. I'd try regenerating the index using samtools and check if it helps.

Also check if anything in the bam header looks suspicious, like the contig shows zero length and things like that.
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