VCF2HAP(1) General Commands Manual VCF2HAP(1) 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 hap- lohseq 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. SEE ALSO haplohseq, ad2vcf, vcf-split, biolibc BUGS Please report bugs to the author and send patches in unified diff format. (man diff for more information) AUTHOR J. Bacon VCF2HAP(1)
NAME | SYNOPSIS | OPTIONS | PURPOSE | DESCRIPTION | SEE ALSO | BUGS | AUTHOR
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