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