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

Poonam Mahapatra
21 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
0

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

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