Difference between revisions of "VcfRefGen"
From Genome Analysis Wiki
Jump to navigationJump to search (Created page with '''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 removi…') |
|||
| Line 1: | Line 1: | ||
| − | ''vcfRefGen | + | ''vcfRefGen'' is a tool for generating VCF reference panels for [http://genome.sph.umich.edu/wiki/minimac 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. |
= Download = | = Download = | ||
Revision as of 15:09, 29 August 2012
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.
Download
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.
|
