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How Do I Pull Out One Read (Given Its Id) From A Bam?

Hi there

Does anyone know how I can pull just one read from a BAM file, when I know the read-id (and sequence) of that read? I'm doing this because I've just got an error saying that one of the reads has no quality information. Since the original BAM is huge, I don't want to convert the whole thing to SAM or fastq and find that read-id. Any suggestions (also on BAM validation) welcome!

cheers Zam

samtools
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updated by Mikael Huss Mikael Huss • written by zam.iqbal.genome zam.iqbal.genome

1 answer

Have you tried piping? E g 

samtools view file.bam | grep read_id

(or using the sequence, in case the read id is somehow inconsistent between FASTQ and BAM as sometimes happens)

• 49 views • link
written by Mikael Huss Mikael Huss

No I haven't, because I didn't want to read the entire file, which is several hundred Gb. Is there a way for grep to just give its first hit? I'll check that...

• 0 views • link
written by zam.iqbal.genome zam.iqbal.genome

grep -m 1 would return the first match and exit.

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written by Vivek Vivek

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