Description

convert between genome builds

Input

name:type
description
pattern

meta:map

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

]

bed:file

Browser Extensible Data (BED) file

*.{bed}

chain:file

Chain file

*.{chain,chain.gz}

Output

name:type
description
pattern

lifted

meta:map

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

]

*.lifted.bed:file

BED file containing successfully lifted variants

*.{lifted.bed}

unlifted

meta:map

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

]

*.unlifted.bed:file

BED file containing variants that couldn’t be lifted

*.{unlifted.bed}

versions

versions.yml:file

File containing software version

versions.yml

Tools

ucsc
varies; see http://genome.ucsc.edu/license

Move annotations from one assembly to another