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?)
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crysis405 •
Use SamToFastq command and set
OUTPUT_PER_RG=TRUE
http://picard.sourceforge.net/command-line-overview.shtml#SamToFastq
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Biomonika (Noolean)
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).
So you are not asking for something more general, you are asking for something in GATK package.
By more general I meant something that doesn't require me to convert SamToFastq
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crysis405 •
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.
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Biomonika (Noolean)
Two independent things. I have merged BAMs so I want to split them and I want to convert BAMs to Fastq.
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