Tools for working with genomic and high throughput sequencing data.
Group: VCF/BCF
Re-genotypes a VCF after downsampling the allele counts.
The input VCF must have at least one sample.
If the input VCF contains a single sample, the downsampling target may be specified as a
proportion of the original read depth using --proportion=(0..1), or as the combination of
the original and target number of sequenced bases (--originalBases and
--downsampleToBases). For multi-sample VCFs, the downsampling target must be specified using
--downsampleToBases, and a metadata file with the total number of sequenced bases per sample
is required as well. The metadata file must follow the
[[https://www.internationalgenome.org/category/meta-data/] 1000 Genomes index format], but the
only required columns are SAMPLE_NAME and BASE_COUNT. A propportion for each sample is
calculated by dividing the target number of sequenced bases by the original number of
sequenced bases.
The tool first (optionally) winnows the VCF file to remove variants within a distance to each
other specified by --window-size (the default value of 0 disables winnowing). Next, each
sample at each variant is examined independently. The allele depths per-genotype are randoml
downsampled given the proportion. The downsampled allele depths are then used to re-compute
allele likelhoods and produce a new genotype.
The tool outputs a downsampled VCF file with the winnowed variants removed, and with the
genotype calls and DP, AD, and PL tags updated for each sample at each retained variant.
| Name | Flag | Type | Description | Required? | Max # of Values | Default Value(s) |
|---|---|---|---|---|---|---|
| input | i | PathToVcf | The vcf to downsample. | Required | 1 | |
| proportion | p | Double | Proportion of bases to retain (for single-sample VCF). | Optional | 1 | |
| original-bases | b | Double | Original number of bases (for single-sample VCF). | Optional | 1 | |
| metadata | m | FilePath | Index file with bases per sample. | Optional | 1 | |
| downsample-to-bases | n | Double | Target number of bases to downsample to. | Optional | 1 | |
| output | o | PathToVcf | Output file name. | Required | 1 | |
| window-size | w | Int | Winnowing window size. | Optional | 1 | 0 |
| epsilon | e | Double | Sequencing Error rate for genotyping. | Optional | 1 | 0.01 |
| write-no-call | c | Boolean | True to write out no-calls. | Optional | 1 | false |
| seed | s | Int | Random seed value. | Optional | 1 | 42 |