How to extract specific location in .bam files
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2.5 years ago

I would like to make a minimal example of my wgs .bam and .bam.bai files to accelerate pipeline testing. For example, i would like to select chr1:1-1e7 & chr1:1-1e7 regions and create that same .bam .bai file from them. How to accomplish that?

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2.5 years ago
GenoMax 142k

Using samtools view : Extract Reads From A Bam File That Fall Within A Given Region Check help page for samtools view for detailed options.

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