Difference between revisions of "VcfRefGen"
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! Description | ! Description | ||
|- | |- | ||
| − | |style=white-space:nowrap|<code>--in < | + | |style=white-space:nowrap|<code>--in <filename></code> |
| − | | Input VCF file. 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] | + | | Input VCF file. 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]. |
|- | |- | ||
| − | | <code>--out < | + | | <code>--out <filename></code> |
| − | | Output VCF filename | + | | Output VCF filename. |
|- | |- | ||
| − | | <code>-- | + | | <code>--uncompress</code> |
| − | | | + | | write an uncompressed VCF output file. |
|- | |- | ||
| − | | <code>-- | + | | <code>--sampleSubset <filename></code> |
| − | | | + | | file with samples IDs to keep (one sample ID per line). |
| + | |- | ||
| + | | <code>--minAC</code> | ||
| + | | minor allele count to keep. | ||
| + | |- | ||
| + | | <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. | ||
| + | |- | ||
| + | | <code>--params</code> | ||
| + | | print the parameter settings | ||
|- | |- | ||
|} | |} | ||
| + | |||
[[Category:Software]] | [[Category:Software]] | ||
Revision as of 15:16, 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 file. The latest 1000 Genomes files can be found here. |
--out <filename>
|
Output VCF filename. |
--uncompress
|
write an uncompressed VCF output file. |
--sampleSubset <filename>
|
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. |
--params
|
print the parameter settings |
