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Document which variantcatalogs to use #443

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Merged
merged 2 commits into from
Nov 15, 2023
Merged

Document which variantcatalogs to use #443

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e155b45
fixes #439
jemten Nov 14, 2023
beb425c
Merge branch 'dev' into document_variantca
jemten Nov 15, 2023
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8 changes: 5 additions & 3 deletions docs/usage.md
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Expand Up @@ -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_catalog<sup>1</sup> | |

<sup>1</sup> 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

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