VCF2HAP

Construct gene haplotype with VCF format files and snpEff annotation.

1. Haplotype format defined in this pipeline

Haplotype created by gatk_vcf_to_haplotype.pl programe contains following files:

• prefix.haplotype containing 6 columns: symbol, haplotype rank, haplotype, annotation, count, samples;
• prefix.vars containing 7 columns: chrom, position, reference allele, alternative allele, covered count, alternative count, annotation;

2. Haplotype format transforming to other data table

• haplotype_to_popart.pl: transforming haplotype to NEXUS format specified for PopART, enabling elegent haplotype network construction and plotting.