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.