update docs

genomic-medicine-sweden · Oct 8, 2024 · f97d4a6 · f97d4a6
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diff --git a/README.md b/README.md
@@ -46,6 +46,7 @@
 
 - Annotate SNVs and INDELs with databases of choice, i.e. [gnomAD](https://gnomad.broadinstitute.org), [CADD](https://cadd.gs.washington.edu) etc. with [echtvar](https://github.com/brentp/echtvar) and [VEP](https://github.com/Ensembl/ensembl-vep)
 - Annotate repeat expansions with [stranger](https://github.com/Clinical-Genomics/stranger)
+- Annotate SVs with [SVDB](https://github.com/J35P312/SVDB) and [VEP](https://github.com/Ensembl/ensembl-vep)
 
 ##### Ranking
 

diff --git a/docs/usage.md b/docs/usage.md
@@ -240,13 +240,22 @@ cadd,/path/to/cadd.v1.6.hg38.zip
 
 This subworkflow relies on the mapping subworkflow, and requires the following additional files:
 
-| Parameter  | Description                                                                                                                                                                                                                              |
-| ---------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `svdb_dbs` | Databases used for structural variant annotation in vcf format. <details><summary>Help</summary><small>Path to comma-separated file containing information about the databases used for structural variant annotation.</small></details> |
+| Parameter               | Description                                                                                                                                                                                                                                            |
+| ----------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| `svdb_dbs` <sup>1</sup> | Csv file with databases used for structural variant annotation in vcf format. <details><summary>Help</summary><small>Path to comma-separated file containing information about the databases used for structural variant annotation.</small></details> |
+
+<sup>1</sup> Example file for input with `--svdb_dbs`:
+
+```
+filename,in_freq_info_key,in_allele_count_info_key,out_freq_info_key,out_allele_count_info_key
+https://github.com/genomic-medicine-sweden/test-datasets/raw/b9ff54b59cdd39df5b6e278a30b08d94075a644c/reference/colorsdb.test_data.vcf.gz,AF,AC,colorsdb_af,colorsdb_ac
+```
+
+These databases could for example come from [CoLoRSdb](https://zenodo.org/records/13145123).
 
 ### Rank variants (`--skip_rank_variants`)
 
-This subworkflow ranks SNVs and INDELs, and relies on the mapping, short variant calling and SNV annotation subworkflows, and requires the following additional files:
+This subworkflow ranks SNVs, and relies on the mapping, short variant calling and SNV annotation subworkflows, and requires the following additional files:
 
 | Parameter            | Description                                                                                                                                                                                                                                                 |
 | -------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |