This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Extracting matching reads by read ID

What tool would you recommend to compare two BAM files and extract matching reads by read ID?

bam
• 3,280 views • link
updated by GenoMax GenoMax • written by Friederike Friederike

Without extracting read names, doing the comparison outside the BAM? filterbyname.sh from BBMap would be an option. You can come up with a clever way of using pipes/process redirection. May post an example later.

• 0 views • link
written by GenoMax GenoMax

Mostly looking for performance-savvy solutions (and general inspiration if there's not a specific tool that would do it)

• 0 views • link
written by Friederike Friederike

well, to be fair, I was mostly searching for a clever way to actually compare two BAM files directly, but it seems I'll have to go via extracting the read names first and then use those for subsetting (which is well covered in those posts)

• 0 views • link
written by Friederike Friederike

2 answers 

samtools view file1.bam | awk -F "\t" '{print $1}' | sort | uniq  > names_in_file1

filterbyname.sh -Xmx4g in=file2.bam names=names_in_file1 out=file.fq.gz include=t

file.fq.gz will include reads that are common in both files.

• 0 views • link
written by GenoMax GenoMax

nice, except that I'd prefer a BAM file in the end, but I think that's an option for filterbyname.sh

• 0 views • link
written by Friederike Friederike

Correct. You can simply use out=filtered.bam.

• 0 views • link
written by GenoMax GenoMax

There is this: https://genome.sph.umich.edu/wiki/BamUtil:_diff

@Pierre also seems to have tool for this: Comparison between .bam files

BAM file comparison

• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this