Description

Converting aligned short and long reads records from one reference to another

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test' ]

input (file)

SAM/BAM/CRAM file to be lifted

*.{bam}

meta_ref (map)

Groovy Map containing reference information
e.g. [ id:'reference' ]

clft (file)

Clft file of indexed ChainMap.

*.{clft}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'reference' ]

bam (file)

Lifted bam file

*.{bam}

versions (file)

File containing software versions

versions.yml

Tools

leviosam2
MIT

Fast and accurate coordinate conversion between assemblies