Pre.py is a preprocessing tool made to preprocess VCF files for Hap.py
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
vcf{:bash}
:file
VCF file to preprocess
*.{vcf,vcf.gz}
bed{:bash}
BED file
*.bed
meta2{:bash}
Groovy Map containing sample information for reference fasta e.g. [ id:‘test2’]
fasta{:bash}
FASTA file of the reference genome
*.{fa,fasta}
meta3{:bash}
Groovy Map containing sample information for reference fai e.g. [ id:‘test3’ ]
fasta_fai{:bash}
The index of the reference FASTA
*.fai
preprocessed_vcf{:bash}
*.vcf.gz{:bash}
Preprocessed VCF file
*.vcf.gz
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Haplotype VCF comparison tools
