awesome :) Thank you! I
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Extract Bamfile using samtools
Hello
It's the first time try to use samtools and I wonder how I can extract bam file by sample.
I need to analyze bam file by Sample and make another BAM file by Sample.
In side of bam file there is sample ID like B1, B2, B3, ... B384.
I wonder if I want to extract only B3 sample from original bam file.
How can I command?
original bam file original.bam -> new bam file b3.bam.
Thank you.
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Ram
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clear.choi •
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clear.choi •
1 answer
using samtools view with the -r option. See the sam spec to understand what is a group-id in a SAM file.
-r STR only include reads in read group STR [null]
samtool view -r B3 -b -o out.bam in.bam
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Pierre Lindenbaum
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Pierre Lindenbaum
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