Extract the alignments from a Bam file by name of the read

Question

[kojix2]

Hello.

I have a question about Bam files. How can I extract the alignment of a specific named read from a Bam file? I did a search for Biostar and and found the following answer

Question: (Closed) Efficiently Extracting Reads With Specific Names ('Queryname') From .Bam File Efficiently Extracting Reads With Specific Names ('Queryname') From .Bam File

samtools view file.bam | grep queryname - > subset.sam

Yes. This is a simple and great answer, but since it's seven years old, I thought there might be a better way today. Is there a more efficient way to extract the Bam files? Especially when they are sorted by name?

(I would like to know how to extract by name and not by location.)

Answer 1

[Pierre Lindenbaum]

FilterSamReads https://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads with READ_LIST_FILE option as I said in C: Extracting Subsets Of Reads From A Bam File

Answer 2

[Jorge Amigo]

If you are looking for a particular read group, you can filter your bam file directly:

samtools view -br RGTAG file.bam > file.RGTAG.bam

If you're looking for a particular read name, parsing the bam file with grep is still a viable way to do it. You can try to optimize it though, if only 1 read is expected:

samtools view file.bam | grep -m1 queryname - > subset.sam

You can try to optimize it even more, if only 1 read is expected and you more or less know the region (say chr3:1000-2000 as an example) where the read could have been mapped:

samtools view file.bam chr3:1000-2000 | grep -m1 queryname - > subset.sam

If you are able to go for this last option, the results should be generated immediately.

[Pierre Lindenbaum]

I would use

grep -F -w -m1

[Jorge Amigo]

You're right. That should be faster and more precise.