vtools issueshttps://git.lumc.nl/klinische-genetica/capture-lumc/vtools/-/issues2019-11-25T12:37:52+01:00https://git.lumc.nl/klinische-genetica/capture-lumc/vtools/-/issues/9vtools-filter has assumptions on chromosome names2019-11-25T12:37:52+01:00van den Bergvtools-filter has assumptions on chromosome namesvtools-filter assumes that canonical chromosomes are called `[1, 2, 3]` or `[chr1, chr2, chr3]`, and uses these contig names when deciding whether or not to filter certain variants. This is most likely not compatible with GRCh38, where t...vtools-filter assumes that canonical chromosomes are called `[1, 2, 3]` or `[chr1, chr2, chr3]`, and uses these contig names when deciding whether or not to filter certain variants. This is most likely not compatible with GRCh38, where the accession number and versions of the chromosomes are used.GRCh38https://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/5alleles_no_call is always 02019-10-22T09:58:41+02:00van den Bergalleles_no_call is always 0vtools-evaluate only looks at calls that are present in both vcf files. Because of this, the alleles_no_call field in the output is always 0. If a record is present in the 'positive' vcf of known calls but missing from the 'called' vcf f...vtools-evaluate only looks at calls that are present in both vcf files. Because of this, the alleles_no_call field in the output is always 0. If a record is present in the 'positive' vcf of known calls but missing from the 'called' vcf file, the alleles_no_call value should be incrementedhttps://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.https://git.lumc.nl/klinische-genetica/capture-lumc/vtools/-/issues/2gcoverage with Bed option in stead of only refflat2019-03-19T10:25:36+01:00Sander Bollengcoverage with Bed option in stead of only refflatSander BollenSander Bollenhttps://git.lumc.nl/klinische-genetica/capture-lumc/vtools/-/issues/1Properties should be named as nouns2019-08-26T10:07:36+02:00Sander BollenProperties should be named as nouns`vtools.stats.Stats` names a property `as_dict`. This should be simply `dict``vtools.stats.Stats` names a property `as_dict`. This should be simply `dict`Sander BollenSander Bollen