Tools for working with genomic and high throughput sequencing data.
Group: VCF/BCF
Assess the accuracy of phasing for a set of variants.
All phased genotypes should be annotated with the PS (phase set) FORMAT tag, which by convention is the
position of the first variant in the phase set (see the VCF specification). Furthermore, the alleles of a phased
genotype should use the | separator instead of the / separator, where the latter indicates the genotype is
unphased.
The input VCFs are assumed to be single sample: the genotype from the first sample is used.
Only bi-allelic heterozygous SNPs are considered.
The input known phased variants can be subsetted using the known interval list, for example to keep only variants from high-confidence regions.
If the intervals argument is supplied, only the set of chromosomes specified will be analyzed. Note that the full chromosome will be analyzed and start/stop positions will be ignored.
| Name | Flag | Type | Description | Required? | Max # of Values | Default Value(s) |
|---|---|---|---|---|---|---|
| called-vcf | c | PathToVcf | The VCF with called phased variants. | Required | 1 | |
| truth-vcf | t | PathToVcf | The VCF with known phased variants. | Required | 1 | |
| output | o | PathPrefix | The output prefix for all output files. | Required | 1 | |
| known-intervals | k | PathToIntervals | The interval list over which known phased variants should be kept. | Optional | 1 | |
| allow-missing-fields-in-vcf-header | m | Boolean | Allow missing fields in the VCF header. | Optional | 1 | true |
| skip-mismatching-alleles | s | Boolean | Skip sites where the truth and call are both called but do not share the same alleles. | Optional | 1 | true |
| intervals | l | PathToIntervals | Analyze only the given chromosomes in the interval list. The entire chromosome will be analyzed (start and end ignored). | Optional | 1 | |
| modify-blocks | b | Boolean | Remove enclosed phased blocks and truncate overlapping blocks. | Optional | 1 | true |
| debug-vcf | d | Boolean | Output a VCF with the called variants annotated by if their phase matches the truth | Optional | 1 | false |