Understand Bedtools coverage output
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2.8 years ago
ramshahaya ▴ 10

I had used bedtools to check coverage.

bedtools coverage -b interval_list.bed -abam fixed.bam -d > bedtools_cov.txt
head -n 2 bedtools_cov.txt 
10  77  112 E00591:309:H7L2KCCX2:6:2215:25712:46630/2   35  -   77  112 0,0,0   1   35, 0,  1   0
10  77  112 E00591:309:H7L2KCCX2:6:2215:25712:46630/2   35  -   77  112 0,0,0   1   35, 0,  2   0

I would like to know which column in the above is for coverage information?

I would like to check coverage for my dataset.

Bedtools coverage • 547 views
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