bam_histo

Format

cg bam_histo ?options? regionfile bamfile ?intervals?

Summary

create a report with coverage data of given regions in a bam file

Description

bam_histo creates a report with the coverage for the region(s) of interest given in regionfile. The report is a tsv file with a line for each region in the region file. Each line will show the number of bases with a coverage (sequencing depth) in the given intervals. It will also show the size of the region and the average, minimum and maximum depth

Arguments

regionfile: region file: tab separated file describing region of interest. Must contain fields: chr, begin, end & name
bamfile: bam file for which a coverage report should be generated
intervals: list (space sperated) of numbers defining the intervals used

Options

-n namecol (-namecol): fieldname (in the region file) to use as name for each row in the result

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