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

Question

[epigene]

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?

Answer 1

[Pierre Lindenbaum]

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

[epigene]

Thanks, will try it out!