Filter hits that aligned concordantly exactly 1 times base on mpq>40

Question

[User000]

Hello,

I need to get all reads that aligned concordantly exactly 1 times base on mpq>40 from hisat2.

samtools view -b -q 40 -o output.bam alignments.bam

Will this command make a job?

Answer 1

[Devon Ryan]

I assume "make a job" means "work". Yes, that will work.

[GenoMax]

Provided samtools was added before view in the command posted :)

[User000]

yes, sorry, I deleted it accidentally before posting! thanks guys