Problems with Picards MarkDuplicates

[nseh]

Hi all,

When running Picards MarkDuplicates I get the following error:

Exception in thread "main" java.lang.RuntimeException: SAM validation error: ERROR: Record 124760536, Read name B80PDAABXX:1:26
:2364:123720#0, MAPQ should be 0 for unmapped read.
at net.sf.samtools.SAMUtils.processValidationErrors(SAMUtils.java:334)
at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:469)
at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:450)
at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:417)
at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:629)
at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:607)
at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:276)
at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:113)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:158)
at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:97)

It says that MAPQ should be 0 for unmapped reads, and this sounds reasonable. But could it be that something went wrong earlier in the analysis? Hope anyone can help!

Nat.

[swbarnes2]

This is a common problem, and you'll run into it with all the Picard suite of tools.

There's a setting that goes something like VALIDATION_STRINGENCY, and if you set it to LENIENT, it will complain about those reads, but it won't stop on them.

This happens with bwa, because it concatenates reference sequence, which leads to slightly odd things happening when a read aligns over the overlap. So this might be the source of your problem. Regardless of what's causing it, you can examine the problem reads, and cut them out, or change the stringency to let them go through.

[nseh]

Thank you! It works