Difference between revisions of "VcfRefGen"
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= Download = | = Download = | ||
− | Source code can in: [[Media:vcfRefGen.0.1.3.tgz|VcfRefGen.0.1.3.tgz]] - Released 01/29/2013 | + | Source code can in: [[Media:vcfRefGen.0.1.4.tgz|VcfRefGen.0.1.4.tgz]] - Released 09/04/2014 |
+ | |||
+ | Older versions: | ||
+ | * [[Media:vcfRefGen.0.1.3.tgz|VcfRefGen.0.1.3.tgz]] - Released 01/29/2013 | ||
= Parameter= | = Parameter= |
Revision as of 15:49, 4 September 2014
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 any additional genotype fields specified in the parameters) and removing any records where any kept sample is not phased or is missing a genotype.
Download
Source code can in: VcfRefGen.0.1.4.tgz - Released 09/04/2014
Older versions:
- VcfRefGen.0.1.3.tgz - Released 01/29/2013
Parameter
Parameter | Description |
---|---|
--in <filename>
|
Input VCF filename. The latest 1000 Genomes files can be found here. |
--out <filename>
|
Output VCF filename. |
--uncompress
|
write an uncompressed VCF output file. |
--sampleSubset <filename>
|
filename of file with samples IDs to keep (one sample ID per line). |
--minAC
|
minor allele count to keep. |
--filterList <filename>
|
filename of file containing regions to include. format: start end start & end positions should be 1-based inclusive positions for SNPs start=end position |
--keepGT <GTs to keep>
|
comma separated list of genotype fields to keep in addition to the GT field |
--params
|
print the parameter settings |
Example
Please find below the command we used for generating MetaboChip specific reference panels from 1000 Genomes data:
foreach chr (`seq 1 22`)
runon -m 1024 vcfRefGen --in ALL.chr$chr.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz \
--out chr$chr.metabo.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz \
--minAC 2 --filterList chr$chr.filter.regions
end
Questions and Comments
Please contact Christian Fuchsberger or Mary Kate Wing