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Old 07-05-2014, 10:25 AM   #21
sdmoore
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Default Possible to add Read Group in BBmap header?

*sorry, probably wrong thread, I found more activity in the release announcement thread*

Hello,
I used BBduk to process my read pairs and then mapped them using BBmap, then sam/bam and sorted.
I plan to use an alternative to mpileup to process this set (for comparison of the outputs), so I am trying to use GATK tools.

When running a GATK tool, it reports the error that the readgoup is not found in the header. With other mappers, this is an option (like -R for BWA). I found a methods to manually add readgoup information to the header (such as here), but I have limited linux skills and get errors when trying that approach (command "header" not found). I am also concerned that if I put the wrong RG info, I may pooch a downstream tool.

Is there a way to make the BBmap output compatible with GATK?

Last edited by sdmoore; 07-05-2014 at 10:34 AM. Reason: wrong thread?
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Old 07-06-2014, 09:25 PM   #22
Brian Bushnell
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sdmoore,

BBMap does not have an option for setting the readgroup, since I never encountered a situation where I needed it. But if it's useful, I can add it to the next release. The solution in your linked thread looks reasonable and I'm not sure why it didn't work for you; I will let you know if I find a better solution.
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Old 07-07-2014, 01:50 AM   #23
dpryan
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@sdmoore: You actually just want AddOrReplaceReadGroups from Picard tools. The command I expect you were going for is "samtools reheader", though that won't really do what you want since read group information is also added to each alignment.

@Brian: It would be great if you could add read group support. That'll be needed by anyone doing SNP calling.
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Old 07-07-2014, 06:53 AM   #24
sdmoore
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Thanks Brian and dpryan.
I had to give up on bbmap for now, not for this problem (I found the AddOrReplaceReadGroups tool later: I edited the sams or the bams). Rather, the resulting vcf from mpileup on the BBmap alignments were "all over the place" (and took forever to process too), I don't know how else to describe it, large insert calls for a bunch of positions. Viewing the file was no help (tons of insert/asterisks displayed). Same mess from FreeBayes. BWA-mem and Bowtie2 assemblies don't show this and I can easily identify known errors in the reference file with either mpileup or freebayes. The assembly looked more like what I got from cushaw2 (and also dropped). We are at a stage now where we will Sanger sequence a few loci to clear things up (e.g., BWA never shows a collection of mutations that Bowtie2 does). I was hoping to have a third assembler "take sides", but I think it's faster for us to sequence and be sure.
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Old 07-07-2014, 10:37 AM   #25
Brian Bushnell
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sdmoore,

By default, BBMap will look for much longer indels than BWA/Bowtie2, over 16000bp. You can limit this with the maxindel flag (e.g. "maxindel=40"). Soft-clipping (via "local" flag) can also reduce erroneous variation calls from chimeric or low-quality reads.
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