BOL: Question: How to extract all the reads mapped at specific region in a genome?

Question: Question: How to extract all the reads mapped at specific region in a genome?

Poonam Mahapatra
2523 days ago

Question: How to extract all the reads mapped at specific region in a genome?

I want to extract all the reads mapped at chr5: 200-6000.

Answers

samtools index your.bam
samtools view your.bam "chr5:200-6000" > output.bam

That would output all reads in chr5 between 200-6000 bp.

Rahul Nayak 2523 days ago