Difference between revisions of "VcfRefGen"
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= Download = | = Download = | ||
Source code can be found [http://www.sph.umich.edu/csg/cfuchsb/ here] . | Source code can be found [http://www.sph.umich.edu/csg/cfuchsb/ here] . | ||
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= Parameter= | = Parameter= | ||
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|style=white-space:nowrap|<code>--in <filename></code> | |style=white-space:nowrap|<code>--in <filename></code> | ||
| − | | Input VCF | + | | Input VCF filename. The latest 1000 Genomes files can be found [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521/phase1_integrated_calls.20101123.ALL.panel here]. |
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| <code>--out <filename></code> | | <code>--out <filename></code> | ||
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| <code>--sampleSubset <filename></code> | | <code>--sampleSubset <filename></code> | ||
| − | | file with samples IDs to keep (one sample ID per line). | + | | filename of file with samples IDs to keep (one sample ID per line). |
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| <code>--minAC</code> | | <code>--minAC</code> | ||
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| <code>--filterList <filename></code> | | <code>--filterList <filename></code> | ||
| − | | filename of file containing regions to include. <br>format: start end <br> start & end positions should be 1-based inclusive positions | + | | filename of file containing regions to include. <br>format: start end <br> start & end positions should be 1-based inclusive positions <br> for SNPs start=end position |
|- | |- | ||
| <code>--params</code> | | <code>--params</code> | ||
Revision as of 15:17, 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 <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 |
--params
|
print the parameter settings |
