VcfRefGen

vcfRefGen' is a tool for generating VCF reference panels for minimac imputation. It reduces VCF files by removing the info field, saving only the GT genotype field and removing any records where any kept sample is not phased or is missing a genotype.

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Source code can be found here .

Parameter

Parameter	Description
--in <file>	Input VCF file. The latest 1000 Genomes files can be found here
--out <file>	Output VCF filename
--states 200	Number of haplotypes to consider during each update. Increasing this value will typically lead to better haplotypes, but can dramatically increase computing time and memory use. A value of 200 - 400 is typical.
--rounds 20	Iterations of the Markov sampler to use for haplotyping. Typically, using 20 - 30 rounds should give good results. To obtain better results, it is usually better to increase the --states parameter.