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