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Is there a tools to select alignment from BAM files with particular tag value?

I'm interested in selecting only uniquely mapped reads from Hisat2 alignment bam files. I think I can do this using the NH tag after reading the post below. I can write a python script to do this. But I'm wondering if there is any existing tools that can do this? i.e. select to output certain alignments if their tag is certain value? in this case, NH:i:1

How to remove non-unique mapping reads with Hisat?

bam
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by epigene epigene

1 answer

using samjs https://github.com/lindenb/jvarkit/wiki/SamJS

java -jar dist/samjs.jar -o out.bam -e 'record.getIntegerAttribute("NH")!=null && record.getIntegerAttribute("NH").intValue()==1'  input.bam
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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks, will try it out!

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written by epigene epigene

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