vtools issueshttps://git.lumc.nl/klinische-genetica/capture-lumc/vtools/-/issues2019-10-08T10:56:07+02:00https://git.lumc.nl/klinische-genetica/capture-lumc/vtools/-/issues/7Add --version command option to vtools2019-10-08T10:56:07+02:00van den BergAdd --version command option to vtoolsFor reproducibility it is important that vtools can print its own version number.For reproducibility it is important that vtools can print its own version number.van den Bergvan den Berghttps://git.lumc.nl/klinische-genetica/capture-lumc/vtools/-/issues/6vtools has no tests2019-10-22T09:58:42+02:00van den Bergvtools has no testsvtools is an important part of the quality control in clinical pipelines, as it is used to compare Array data with the called genotypes. However, there are currently no automated tests to verify that vtools performs as expected.vtools is an important part of the quality control in clinical pipelines, as it is used to compare Array data with the called genotypes. However, there are currently no automated tests to verify that vtools performs as expected.van den Bergvan den Berghttps://git.lumc.nl/klinische-genetica/capture-lumc/vtools/-/issues/4Add optional gvcf file to vtools-evaluate2019-08-26T18:12:18+02:00van den BergAdd optional gvcf file to vtools-evaluateCurrently, `vtools-evaluate` uses compares two VCF files. However, the typical use case is to compare a set of known variants (for example from an OpenArray) to the variants found using NGS sequencing. In this context, the known variants...Currently, `vtools-evaluate` uses compares two VCF files. However, the typical use case is to compare a set of known variants (for example from an OpenArray) to the variants found using NGS sequencing. In this context, the known variants can contain sites that are either:
1. called as homref in the g.vcf file
2. are missing completely from the NGS data
These two cases should not be treated the same (as 'missing data'). When a g.vcf file is specified, the homref calls in this file can be matched against the calls in the OpenArray file.