Commit 21db43a3 authored by Sander Bollen's avatar Sander Bollen
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evaluate docs

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......@@ -101,4 +101,33 @@ Options:
--help Show this message and exit.
### vtools-evaluate
Evaluate a VCF file to a baseline VCF file containing true positives.
We only consider variants that are present in both VCF files. This makes
it useful when the two VCF files have been produced by wildly different
technologies. E.g, when comparing a WES VCF file vs a SNP array, this
tool can be quite useful.
Output is a simple JSON file listing counts of concordant and discordant
vtools-evaluate only considers one sample. Multisample VCF files are allowed;
the sample to be evaluated has to be set through a CLI argument.
#### Usage
Usage: vtools-evaluate [OPTIONS]
-c, --call-vcf PATH Path to VCF with calls to be evaluated
-p, --positive-vcf PATH Path to VCF with known calls [required]
-cs, --call-samples TEXT Sample(s) in call-vcf to consider. May be
called multiple times [required]
-ps, --positive-samples TEXT Sample(s) in positive-vcf to consider. May be
called multiple times [required]
--help Show this message and exit.
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