How do I filter a BAM file for proper pairs WITHOUT samtools

Question

[hohoku]

I need to remove unpaired reads from my BAM file... and I'm looking for a non-samtools way of doing it. Suggestions?

[finswimmer]

May I ask you why samtools is not allowed?

[hohoku]

We have some conflicts with samtools

[Devon Ryan]

That's incredibly unusual, it's likely you should just fix your environment then.

[hohoku]

I would normally agree, but we have reasons for not using samtools in this instance

Answer 1

[Devon Ryan]

In deepTools:

alignmentSieve --samFlagInclude 2 -b input.bam -o output.bam

You can use multiple threads if you like. Of course this uses pysam, which uses htslib, which is part of samtools, but most tools will use something related to samtools somewhere...it's a standard tool after all.

Answer 2

[Pierre Lindenbaum]

using samjdk http://lindenb.github.io/jvarkit/SamJdk.html

java -jar  dist/samjdk.jar -e 'return record.getProperPairFlag();' input.bam

Answer 3

[hohoku]

Thanks for the above responses, but we also found Sambamba which is pretty fast sambamba view -f bam -F "proper_pair" -o output.bam input.bam