bedCoverage

Category

Genomic Interval Manipulation

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Usage

bedCoverage genomeDatabase bedFile

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Manual

This tool is part of UCSC Genome Browser's utilities.

Required arguments

• genomeDatabase string: Genome assembly that the input regions are defined in. Must be in the list of UCSC Genome Browser database genomes. If a genome is not included in UCSC's database (e.g. gX), you will observe errors like

  Couldn't connect to database hg64 on genome-mysql.soe.ucsc.edu as genomep.
  Unknown database 'gX'

• bedFile string: Bed file for the calculation of genome-wide coverage. Note bed file must be sorted by chromosome.

Options

• -restrict=string: Restrict to parts in this file.

Examples

$ bedCoverage hg38 enC.bed | head
chr1   230486321 depth   22825283  9.90 anyCov   22825283  9.90%
 1    22825283 9.903%
 2           0 0.000%
 3           0 0.000%
 4           0 0.000%
 5           0 0.000%
 6           0 0.000%
 7           0 0.000%
 8           0 0.000%
 9           0 0.000%

File formats this tool works with

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