Lifts over a VCF file from one reference build to another.
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input_vcf
:file
VCF file
*.{vcf,vcf.gz}
meta2
Groovy Map containing reference information e.g. [ id:‘genome’ ]
dict
dictionary for fasta file
*.{dict}
meta3
fasta
fasta file
*.fasta
meta4
chain
The liftover chain file
vcf_lifted
*.lifted.vcf.gz
VCF file containing successfully lifted variants
*.{lifted.vcf.gz}
vcf_unlifted
*.unlifted.vcf.gz
VCF file containing unsuccessfully lifted variants
*.{unlifted.vcf.gz}
versions_picard
${task.process}
:string
The process the versions were collected from
picard
The tool name
picard LiftoverVcf --version 2>&1 | sed -n 's/.*Version://p'
The command used to generate the version of the tool
versions
Move annotations from one assembly to another
