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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 haplo- type 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 for- mat. (man diff for more information) AUTHOR J. Bacon VCF2HAP(1)
NAME | SYNOPSIS | OPTIONS | PURPOSE | DESCRIPTION | SEE ALSO | BUGS | AUTHOR
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