NAME

VCF2HAP - Generate haplotype file from a VCF

SYNOPSIS

vcf2hap [--xz] sample-ID < sample.vcf[.xz] > sample.hap
bcftools view sample.bcf | vcf2hap sample-ID > sample.hap

OPTIONS

--xz: VCF input is compressed with xz

PURPOSE

vcf2hap is a simple tool for generating a .hap file as required by haplohseq from a VCF input, which is assumed to be phased.

DESCRIPTION

The sample-ID provided on the command line is a arbitary string which will be included in the .hap output.

Specify the --xz flag if the input is xz-compressed.

vcf2hap is extremely fast (about 19 times faster than format_hap.py) and requires a trivial amount of memory regardless of the size of the VCF file. Performance is important as it is often necessary to haplotype tens of thousands of large VCF files.

BUGS

Please report bugs to the author and send patches in unified diff format. (man diff for more information)

AUTHOR

J. Bacon