How to extract reads from specified area of bam/sam file

Editor to share with you how to extract the bam/sam file designated area reads, I believe that most people do not know much, so share this article for your reference, I hope you can learn a lot after reading this article, let's go to know it!

If you want to extract reads from a sam or bam file within a specified area, you can use samtools and bedtools.

First prepare a zone information file. Region.bed # is listed as the first chromosome ID, and the second and third columns are the starting and ending positions, respectively.

Example: 12 21100 41200 # take the sequence of chromosome 12 between 21100 and 41200

After that, if it is a sam file, convert it to a bam file:

Samtools view-Sb reads.sam > reads.bam

You can then use bedtools to extract the reads, with the following command:

Bedtools intersect-a reads.bam-b region.bed > target_reads.bam

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