Oh great !!
Thanks a lot !
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You only need the header, so no need to output the whole thing.Code:samtools view -H ${OUTPUT}.bam | grep "^@RG" >RG_${OUTPUT}Leave a comment:
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Obtain Read Group from Bam file
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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