diff --git a/docs/usage.md b/docs/usage.md index 311dc349..75a8a1e5 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -176,9 +176,11 @@ The mandatory and optional parameters for each category are tabulated below. ##### 3. Repeat expansions -| Mandatory | Optional | -| --------------- | -------- | -| variant_catalog | | +| Mandatory | Optional | +| --------------------------- | -------- | +| variant_catalog1 | | + +1 We reccomend using the catalogs found [here](https://github.com/Clinical-Genomics/reference-files/tree/master/rare-disease/disease_loci/ExpansionHunter-v5.0.0). These catalogs have been extended from the illumina ones to include information on pathogenicity, which is neccesarry for the workflow. ##### 4. Variant calling - SNV