This PR adds a new feature that allows the usage of more complex filter definitions for VCF files as discussed in issue #21 .
vembrane tag tags variants by specific filter criteria within the FILTER column of the VCF files.
The parameter --custom_filters controls this feature. It specified a TSV file, for which an example is deposited in assets/custom_filters.tsv, that has information about filter names and their respective filter criteria. It can follow python syntax as specified for vembrane filter (see also vembrane docs). All filters specified here will be tagged in the VCF file.
vembrane filter creates additional VCF file with variants filtered based on the specific filter.
The parameter --used_filters controls this feature. It accepts filter names present in the FILTER column of the VCF file. It will create additional VCF files with the respective FILTER subset (i.e., including all variants with the respective tag) that will be further processed downstream, generating separate TSV and HTML files. the unfiltered VCF will also be provided, i.e. this filter does not prevent the output of full VCF file reports.
Future goals:
Enable combining filters more easily, e.g. by just defining "pathogenic and high_quality" or "BRCAgenes or EMTgenes"
Implements custom, predefined filters
This PR adds a new feature that allows the usage of more complex filter definitions for VCF files as discussed in issue #21 .
vembrane tagtags variants by specific filter criteria within the FILTER column of the VCF files. The parameter--custom_filterscontrols this feature. It specified a TSV file, for which an example is deposited in assets/custom_filters.tsv, that has information about filter names and their respective filter criteria. It can follow python syntax as specified for vembrane filter (see also vembrane docs). All filters specified here will be tagged in the VCF file.vembrane filtercreates additional VCF file with variants filtered based on the specific filter. The parameter--used_filterscontrols this feature. It accepts filter names present in the FILTER column of the VCF file. It will create additional VCF files with the respective FILTER subset (i.e., including all variants with the respective tag) that will be further processed downstream, generating separate TSV and HTML files. the unfiltered VCF will also be provided, i.e. this filter does not prevent the output of full VCF file reports.Future goals: