Commit 335925d5 authored by van den Berg's avatar van den Berg
Browse files

Merge branch 'testing' into 'devel'

Merge testing into master

See merge request !6
parents 5b51b794 e6309163
Pipeline #2875 failed with stage
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......@@ -4,4 +4,5 @@ build:
- docker
script:
- pip install --upgrade pip setuptools wheel
- pip install '.'
- pip install cython numpy
- tox
......@@ -135,11 +135,15 @@ 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
alleles.
alleles and some other metrics. It is also possible to output the discordant
VCF records.
Multisample VCF files are allowed; the samples to be evaluated have to be set
through a CLI argument.
Variants from the `--call-vcf` are filtered to have a Genotype Quality (GQ) of
at least 30 by default. This can be overruled by specifying `--min-qual 0`.
The optional flag `--min-depth` can be used to set the minimum read coverage.
#### Usage
......@@ -154,10 +158,12 @@ Options:
called multiple times [required]
-ps, --positive-samples TEXT Sample(s) in positive-vcf to consider. May be
called multiple times [required]
-s, --stats PATH Path to output stats json file [required]
-dc, --discordant PATH Path to output discordant VCF file
--help Show this message and exit
```
-s, --stats PATH Path to output stats json file
-dc, --discordant PATH Path to output gzipped discordant vcf file
-mq, --min-qual FLOAT Minimum quality of variants to consider
-md, --min-depth INTEGER Minimum depth of variants to consider
--help Show this message and exit.
```
## License
......
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