Question: How do I filter a BAM file for proper pairs WITHOUT samtools
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Devon Ryan ♦ 96k wrote:
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.
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Pierre Lindenbaum ♦ 130k wrote:
using samjdk http://lindenb.github.io/jvarkit/SamJdk.html
java -jar dist/samjdk.jar -e 'return record.getProperPairFlag();' input.bam
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May I ask you why samtools is not allowed?
We have some conflicts with samtools
That's incredibly unusual, it's likely you should just fix your environment then.
I would normally agree, but we have reasons for not using samtools in this instance