Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update docs #594

Merged
merged 4 commits into from
Aug 14, 2024
Merged

Update docs #594

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
6dd5f0a
Corrects usage docs
ramprasadn Aug 13, 2024
0c5b700
update changelog
ramprasadn Aug 13, 2024
151e909
fix lint
ramprasadn Aug 13, 2024
01a7b42
Merge branch 'dev' into update-docs
ramprasadn Aug 14, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- Update docs to show 'vep_plugin_files' as a mandatory parameter for SNV annotation [#594](https://github.com/nf-core/raredisease/issues/593)
- Error in SVDB merge when only a single SV caller is run [#586](https://github.com/nf-core/raredisease/pull/586)
- Errors due to misplaced version statements [#578](https://github.com/nf-core/raredisease/pull/578)
- Stub crashes due to peddy reported in [#566](https://github.com/nf-core/raredisease/issues/566) [#576](https://github.com/nf-core/raredisease/pull/576]
Expand Down
29 changes: 15 additions & 14 deletions docs/usage.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -228,16 +228,17 @@ The mandatory and optional parameters for each category are tabulated below.

##### 7. SNV annotation & Ranking

| Mandatory | Optional |
| ------------------------------------ | --------------------------------------------- |
| genome<sup>1</sup> | reduced_penetrance<sup>8</sup> |
| vcfanno_resources<sup>2</sup> | vcfanno_lua |
| vcfanno_toml<sup>3</sup> | vep_filters/vep_filters_scout_fmt<sup>9</sup> |
| vep_cache_version | cadd_resources<sup>10</sup> |
| vep_cache<sup>4</sup> | vep_plugin_files<sup>11</sup> |
| gnomad_af<sup>5</sup> | |
| score_config_snv<sup>6</sup> | |
| variant_consequences_snv<sup>7</sup> | |
| Mandatory | Optional |
| ------------------------------------ | ---------------------------------------------- |
| genome<sup>1</sup> | reduced_penetrance<sup>9</sup> |
| vcfanno_resources<sup>2</sup> | vcfanno_lua |
| vcfanno_toml<sup>3</sup> | vep_filters/vep_filters_scout_fmt<sup>10</sup> |
| vep_cache_version | cadd_resources<sup>11</sup> |
| vep_cache<sup>4</sup> | |
| gnomad_af<sup>5</sup> | |
| score_config_snv<sup>6</sup> | |
| variant_consequences_snv<sup>7</sup> | |
| vep_plugin_files<sup>8</sup> | |

<sup>1</sup>Genome version is used by VEP. You have the option to choose between GRCh37 and GRCh38.<br />
<sup>2</sup>Path to VCF files and their indices used by vcfanno. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/vcfanno_resources.txt).<br />
Expand All @@ -249,10 +250,10 @@ See example cache [here](https://raw.githubusercontent.com/nf-core/test-datasets
no header and the following columns: `CHROM POS REF_ALLELE ALT_ALLELE AF`. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/gnomad_reformated.tab.gz).<br />
<sup>6</sup>Used by GENMOD for ranking the variants. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/rank_model_snv.ini).<br />
<sup>7</sup>File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic and mitochondrial SNVs. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/variant_consequences_v2.txt). You can learn more about these terms [here](https://grch37.ensembl.org/info/genome/variation/prediction/predicted_data.html).
<sup>8</sup>Used by GENMOD while modeling the variants. Contains a list of loci that show [reduced penetrance](https://medlineplus.gov/genetics/understanding/inheritance/penetranceexpressivity/) in people. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/reduced_penetrance.tsv).<br />
<sup>9</sup> This file contains a list of candidate genes (with [HGNC](https://www.genenames.org/) IDs) that is used to split the variants into canditate variants and research variants. Research variants contain all the variants, while candidate variants are a subset of research variants and are associated with candidate genes. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/hgnc.txt). Not required if --skip_vep_filter is set to true.<br />
<sup>10</sup>Path to a folder containing cadd annotations. Equivalent of the data/annotations/ folder described [here](https://github.com/kircherlab/CADD-scripts/#manual-installation), and it is used to calculate CADD scores for small indels. <br />
<sup>11</sup>A CSV file that describes the files used by VEP's named and custom plugins. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/vep_files.csv). <br />
<sup>8</sup>A CSV file that describes the files used by VEP's named and custom plugins. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/vep_files.csv). <br />
<sup>9</sup>Used by GENMOD while modeling the variants. Contains a list of loci that show [reduced penetrance](https://medlineplus.gov/genetics/understanding/inheritance/penetranceexpressivity/) in people. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/reduced_penetrance.tsv).<br />
<sup>10</sup> This file contains a list of candidate genes (with [HGNC](https://www.genenames.org/) IDs) that is used to split the variants into canditate variants and research variants. Research variants contain all the variants, while candidate variants are a subset of research variants and are associated with candidate genes. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/hgnc.txt). Not required if --skip_vep_filter is set to true.<br />
<sup>11</sup>Path to a folder containing cadd annotations. Equivalent of the data/annotations/ folder described [here](https://github.com/kircherlab/CADD-scripts/#manual-installation), and it is used to calculate CADD scores for small indels. <br />

:::note
We use CADD only to annotate small indels. To annotate SNVs with precomputed CADD scores, pass the file containing CADD scores as a resource to vcfanno instead. Files containing the precomputed CADD scores for SNVs can be downloaded from [here](https://cadd.gs.washington.edu/download) (download files listed under the description: "All possible SNVs of GRCh3<7/8>/hg3<7/8>")
Expand Down