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bedtools genomecov for a specific set of chromosomes

Open vkkodali opened this issue 1 year ago • 0 comments

I am trying to compute genome coverage starting from a bam file. By default bedtools genomecov computes coverage for the entire genome. Is there a way to restrict this to a specific set of ranges? I tried adding -g <genome> to restrict the output to a specific set of chromosomes but the genome files are ignored when a bam is used as input.

vkkodali avatar Mar 16 '23 19:03 vkkodali