diff --git a/README.md b/README.md index bc59d979..c33a005f 100644 --- 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 index a52cd3b9..ff893687 100644 --- 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.
HelpPath to comma-separated file containing information about the databases used for structural variant annotation.
| +| Parameter | Description | +| ----------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | +| `svdb_dbs` 1 | Csv file with databases used for structural variant annotation in vcf format.
HelpPath to comma-separated file containing information about the databases used for structural variant annotation.
| + +1 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 | | -------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |