Question

Split merged BAM file

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10.5 years ago

crysis405 ▴ 30

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?)

fastQ bam • 2.3k views

ADD COMMENT • link updated 3.1 years ago by Ram 44k • written 10.5 years ago by crysis405 ▴ 30

Ram · Answer 1 · 2014-06-10

1

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10.5 years ago

Biomonika (Noolean) 3.2k

Use SamToFastq command and set

OUTPUT_PER_RG=TRUE

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

ADD COMMENT • link updated 5.1 years ago by Ram 44k • written 10.5 years ago by Biomonika (Noolean) 3.2k

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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).

ADD REPLY • link 10.5 years ago by crysis405 ▴ 30

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

ADD REPLY • link 10.5 years ago by Biomonika (Noolean) 3.2k

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

ADD REPLY • link updated 4.9 years ago by Ram 44k • written 10.5 years ago by crysis405 ▴ 30

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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.

ADD REPLY • link updated 4.9 years ago by Ram 44k • written 10.5 years ago by Biomonika (Noolean) 3.2k

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

ADD REPLY • link 10.5 years ago by crysis405 ▴ 30