Obtain Read Group from Bam file

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MurielGB

Member

Join Date: Oct 2013

Posts: 51
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#1

Obtain Read Group from Bam file

01-17-2014, 02:19 AM

Hello,
Is it possible to obtain the read group of a bam file ?
I am doing this by converting bam into sam (see below) but I would like to do it directly on the bam file because converting is long !
Thanks a lot !

#samtools view -h ${OUTPUT}.bam > ${OUTPUT}.bam.sam
#grep "^@RG" ${OUTPUT}.bam.sam > RG_${OUTPUT}
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dpryan

Devon Ryan

Join Date: Jul 2011

Posts: 3478
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#2

01-17-2014, 03:11 AM

Code:

samtools view -H ${OUTPUT}.bam | grep "^@RG" >RG_${OUTPUT}

You only need the header, so no need to output the whole thing.
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MurielGB

Member

Join Date: Oct 2013

Posts: 51
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#3

01-17-2014, 03:13 AM

Oh great !!
Thanks a lot !
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