Question: Picard MergeBamAlignment error - record in unmapped BAM is not second of pair
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gravatar for freuv1
12 weeks ago by
freuv110
freuv110 wrote:

Hi,

I am using Picard MergeBamAlignment to merge an unaligned BAM (uBAM) file with an aligned SAM file.

I used ValidateSamFile and FixMateInformation to edit mate pair errors in the uBAM and SAM files.

However, the following is the error I keep running into:

Exception in thread "main" net.sf.picard.PicardException: Second record in unmapped bam is not second of pair: ST-K00112:15:HKFFTBBXX:1:1101:10003:16084

I then ran ValidateSamFile on the uBAM and it yielded several errors that were one of the following:

Both mates are marked as first of pair Both mates are marked as second of pair

Please advise how I can rectify this.

ADD COMMENTlink modified 29 days ago by Biostar ♦♦ 20 • written 12 weeks ago by freuv110
net.sf.picard.PicardException

Your version of picard too old: should be picard.PicardException ( https://github.com/broadinstitute/picard/blob/master/src/main/java/picard/PicardException.java )

ADD REPLYlink written 29 days ago by Pierre Lindenbaum101k
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