Description

Chromograph is a python package to create PNG images from genetics data such as BED and WIG files.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

autozyg:file

Bed file containing the regions of autozygosity

meta2:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

coverage:file

Wig file containing the coverage information

meta3:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

exome:file

Bed file containing the coverage for exome.

meta4:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

fracsnp:file

Wig file containing the fraction of homozygous SNPs

meta5:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

ideogram:file

Bed file containing information necessary for ideogram plots. Format [‘chrom’, ‘start’, ‘end’, ‘name’, ‘gStain’]

meta6:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

regions:file

Bed file containing UPD regions

meta7:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

sites:file

Bed file containing UPD sites

Output

name:type
description
pattern

plots

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}:file

Directory containing the plots in png format

*.png

versions

versions.yml:file

File containing software versions

versions.yml

Tools

chromograph
MIT

Chromograph is a python package to create PNG images from genetics data such as BED and WIG files.

github.com/Clinical-Genomics/chromograph github.com/Clinical-Genomics/chromograph/blob/master/README.md
raredisease
Github user ramprasadn
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