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Update docs #594

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Aug 14, 2024
Merged

Update docs #594

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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
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1 change: 1 addition & 0 deletions CHANGELOG.md
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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]
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29 changes: 15 additions & 14 deletions docs/usage.md
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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>")
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