Converting aligned short and long reads records from one reference to another
meta:map
Groovy Map containing sample information e.g. [ id:'test' ]
[ id:'test' ]
input:file
SAM/BAM/CRAM file to be lifted
*.{bam}
meta_ref:map
Groovy Map containing reference information e.g. [ id:'reference' ]
[ id:'reference' ]
clft:file
Clft file of indexed ChainMap.
*.{clft}
bam
Groovy Map containing sample information e.g. [ id:'reference' ]
*.bam:file
Lifted bam file
versions
versions.yml:file
File containing software versions
versions.yml
Fast and accurate coordinate conversion between assemblies
