Add option to take a whitelist of variants

[jemten]

Description of feature

Right now we have the option of filtering the vcf to remove common mutations as they are very unlikely to cause a rare disease. However, some mutations are quite common and can still cause serious effects, one such example is founder mutations. It would be useful to be able to provide a vcf with variants that should never be filtered, i.e. a whitelist. These variants should then be rescued from the filtering happening here

raredisease/subworkflows/local/annotate_snvs.nf

Line 79 in c371602

BCFTOOLS_VIEW(ZIP_TABIX_VCFANNO.out.gz_tbi, [], [], []) // filter on frequencies

[ramprasadn]

This is managed variants, right @jemten?

[jemten]

Exactly! Will close the issue since it has been implemented