How to extract unique mapped results from BWA results?

Question

[zhwjmch]

How to extract unique mapped results from BWA results?

I am working with 454 data, and I chose BWA mem as the mapping tool.

Thanks in advance.

[Pierre Lindenbaum]

duplicate of Bwa-Mem: Discriminate Between Reads Mapping Uniquely And Those Mapping In Multiple Positions

Answer 1

[Paul]

Hi man,

did you try samtools + grep funciton in terminal?

samtools view your_bwa.bam | grep "XT:A:U" > my_unique.sam

Best,

Paul.

[chefarov]

This produces empty file in my case, whereas if I try this on the equivalent sam file:

grep -E "@|NM:" my.sam | grep -v "XS:" > my.sam.unique

seems to work. However my sam is produced by bowtie2 (if that's the cause of the confusion)