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