Hey Ben,
the resulting SAM should not have a trailing "/1" or "/2", and if that is
the case using SamToFastq, then I believe that is a bug. Could you send a
minimal test case and I can help debug?
N
On Fri, Nov 7, 2014 at 9:44 AM, Ben Bimber <bbim...@gmail.com> wrote:
> I am using picard's MergeBamAlignment w/ a BAM generated by bwa-sw and
> illumina paired-end FASTQ data. Note: the reads contain trailing a "/1" or
> "/2" in the names. The process is:
>
> 1) generate BAM using bwa-sw. When this runs, the resulting BAM has
> alignments names that stripped off the trailing "/1" or "/2".
> 2) use FastqToSam to convert all reads from FASTQ1 + FASTQ2 into a single
> SAM. The read name contain trailing a "/1" or "/2".
> 3) run MergeBamAlignment using the BAMs created above
>
> I believe the problem is that the names dont match up. I get an error
> along the lines of:
>
> 07 Nov 2014 14:19:13,639 DEBUG: Exception in thread "main"
> java.lang.IllegalStateException: Aligned record iterator
> (M00370:96:000000000-AAU0P:1:1101:10136:22111) is behind the unmapped reads
> (M00370:96:000000000-AAU0P:1:1101:10136:22111/1)
> 07 Nov 2014 14:19:13,643 DEBUG: at
> picard.sam.AbstractAlignmentMerger.mergeAlignment(AbstractAlignmentMerger.java:375)
> 07 Nov 2014 14:19:13,646 DEBUG: at
> picard.sam.SamAlignmentMerger.mergeAlignment(SamAlignmentMerger.java:173)
> 07 Nov 2014 14:19:13,650 DEBUG: at
> picard.sam.MergeBamAlignment.doWork(MergeBamAlignment.java:244)
> 07 Nov 2014 14:19:13,654 DEBUG: at
> picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:183)
> 07 Nov 2014 14:19:13,659 DEBUG: at
> picard.sam.MergeBamAlignment.main(MergeBamAlignment.java:213)
> 07 Nov 2014 14:19:13,664 WARN : process exited with non-zero value: 1
>
> Looking at the code, we have 2 iterators, each running over the alignment
> names in the respective BAMs. One is using names w/o the trailing numbers
> and one kept them. I see options like STRIP_UNPAIRED_MATE_NUMBER in
> FastqToSam, but that doesnt seem like it applies to my paired end FASTQs.
> Did I miss a step or option in preparing these files? Is there a standard
> way to handle this?
>
> Thanks for any help.
>
> -Ben
>
>
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