Question

Per Base Coverage

0

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12.7 years ago

Info_Nowise ▴ 10

Is there a way to obtain per-base coverage for a define chromosome interval using a bam file generated from Illumina single-end reads? genomeCoverageBed in Bedtools does not seem to have an option for it.

bedtools coverage • 4.3k views

ADD COMMENT • link updated 12.7 years ago by Aaronquinlan 12k • written 12.7 years ago by Info_Nowise ▴ 10

Ram · Answer 1 · 2012-03-09

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12.7 years ago

Zev.Kronenberg 12k

samtools depth your.bam

ADD COMMENT • link updated 4.7 years ago by Ram 44k • written 12.7 years ago by Zev.Kronenberg 12k

Ram · Answer 2 · 2012-03-09

4

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12.7 years ago

Aaronquinlan 12k

Also,

bedtools coverage -abam aln.bam -b regions.bed -d

ADD COMMENT • link updated 4.7 years ago by Ram 44k • written 12.7 years ago by Aaronquinlan 12k