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


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 2.3 years ago by Biostar ♦♦ 20 • written 2.5 years ago by freuv110

Your version of picard too old: should be picard.PicardException ( )

ADD REPLYlink written 2.3 years ago by Pierre Lindenbaum126k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1527 users visited in the last hour