Split merged BAM file

Question

[crysis405]

I need to revert a BAM file back to FastQ. Based on the GATK guide I need to shuffle first and then convert: http://www.broadinstitute.org/gatk/guide/article?id=2908

However, they don't mention anything about merged BAM files.

How do you split a BAM file by read group information? (Is it possible with Picardtools or samtools?)

Answer 1

[Biomonika (Noolean)]

Use SamToFastq command and set

OUTPUT_PER_RG=TRUE

http://picard.sourceforge.net/command-line-overview.shtml#SamToFastq

[crysis405]

Is there a more general utility? Like if I need to split a merged file from GATK BQSR by read group when I want to run reducedreads? Are there any alternatives to BamUtils splitBam (I am sure there must by something that the GATK team use to do this).

[Biomonika (Noolean)]

So you are not asking for something more general, you are asking for something in GATK package.

[crysis405]

By more general I meant something that doesn't require me to convert SamToFastq

[Biomonika (Noolean)]

I am sorry, I dont understand. You wanted to revert a BAM file back to FastQ and SamToFastq can work with BAM files instead of SAM files as well.

[crysis405]

Two independent things. I have merged BAMs so I want to split them and I want to convert BAMs to Fastq.