Update documentation (#231)

* Documentation draft * Add oncokb in documents * Update oncokb columns in documents * Update oncokb token format * Update docs with config setting examples
genome-nexus · Aug 8, 2023 · db9670d · db9670d
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@@ -77,6 +77,110 @@ Make sure to adjust the file paths according to your specific requirements. Once
 | `-a` | `--add-original-genomic-location` | Add original genomic location data columns into the output, name columns with prefix 'IGNORE_Genome_Nexus_Original_'). This would be useful if saving a reference of original input is needed and won't be changed in any condition|
 | `-d` | `--ignore-original-location` | Genome-nexus-annotation-pipeline reads original genomic location info as input by default, if not existing, reading from normal genomic location info columns. Adding `-d` ignores original genomic location info columns (columns with prefix 'IGNORE_Genome_Nexus_Original_') and only use whatever in normal genomic location info columns. This would be helpful if you'd like to stick with current genomic location info columns.|
 
+### Annotation fields
+| Field | Source | Note |
+| --| -- | -- |
+| Hugo_Symbol |||
+|Entrez_Gene_Id|||
+|Center|||
+|NCBI_Build|||
+|Chromosome|GN response / Input||
+|Start_Position|GN response / Input||
+|End_Position|GN response / Input||
+|Strand|||
+|Consequence|||
+|Variant_Classification|||
+|Variant_Type|||
+|Reference_Allele|GN response / Input||
+|Tumor_Seq_Allele1|||
+|Tumor_Seq_Allele2|GN response / Input||
+|dbSNP_RS|||
+|dbSNP_Val_Status|||
+|Tumor_Sample_Barcode|||
+|Matched_Norm_Sample_Barcode|||
+|Match_Norm_Seq_Allele1|||
+|Match_Norm_Seq_Allele2|||
+|Tumor_Validation_Allele1|||
+|Tumor_Validation_Allele2|||
+|Match_Norm_Validation_Allele1|||
+|Match_Norm_Validation_Allele2|||
+|Verification_Status|||
+|Validation_Status|||
+|Mutation_Status|||
+|Sequencing_Phase|||
+|Sequence_Source|||
+|Validation_Method|||
+|Score|||
+|BAM_File|||
+|Sequencer|||
+|t_ref_count|||
+|t_alt_count|||
+|n_ref_count|||
+|n_alt_count|||
+|HGVSc|||
+|HGVSp|||
+|HGVSp_Short|||
+|Transcript_ID|||
+|RefSeq|VEP||
+|Protein_position|VEP||
+|Codons|VEP||
+|Exon_Number|VEP||
+|gnomAD_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
+|gnomAD_AFR_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
+|gnomAD_AMR_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
+|gnomAD_ASJ_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
+|gnomAD_EAS_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
+|gnomAD_FIN_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
+|gnomAD_NFE_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
+|gnomAD_OTH_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
+|gnomAD_SAS_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
+|MA:FIS|Mutation Assessor|Need to add "mutation_assessor" in "genomenexus.enrichment_fields"|
+|MA:FImpact|Mutation Assessor|Need to add "mutation_assessor" in genomenexus.enrichment_fields"|
+|MA:link.MSA|Mutation Assessor|Need to add "mutation_assessor" in "genomenexus.enrichment_fields"|
+|MA:link.PDB|Mutation Assessor|Need to add "mutation_assessor" in "genomenexus.enrichment_fields"|
+|Polyphen_Prediction|Polyphen|Need to add "polyphen" in "genomenexus.enrichment_fields"|
+|Polyphen_Score|Polyphen|Need to add "polyphen" in "genomenexus.enrichment_fields"|
+|SIFT_Prediction|SIFT|Need to add "sift" in "genomenexus.enrichment_fields"|
+|SIFT_Score|SIFT|Need to add "sift" in "genomenexus.enrichment_fields"|
+|Ref_Tri||Need to add "nucleotide_context" in "genomenexus.enrichment_field"|
+|Var_Tri||Need to add "nucleotide_context" in "genomenexus.enrichment_field"|
+|oncokb_geneExist|OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
+|oncokb_highestDXLevel|OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
+|oncokb_highestPXLevel|OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
+|oncokb_highestResistanceLevel|OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
+| oncokb_highestSensitiveLevel |OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
+| oncokb_mutationEffect|OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
+|oncokb_mutationEffectCitations|OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
+| oncokb_oncogenic|OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
+| oncokb_variantExist   |OncoKb|Need to add "oncokb" in "genomenexus.enrichment_fields" and provide your OncoKB token in "oncokb.token"|
+|Annotation_Status||FAILED / SUCCESS|
+
+
+### Add additional annotation columns
+Genome Nexus supports additional annotation columns with the setting of "enrichment_fields". The configuration for these enrichment fields is managed through the `application.properties` file, please refer to `Pre-build steps` section.
+To configure the enrichment fields, you need to include the desired field names from the provided list in the `-Dgenomenexus.enrichment_fields=` parameter of the command line, or directly add field names in `genomenexus.enrichment_fields=` in `application.properties` file. Multiple field names can be specified by separating them with commas. `annotation_summary` is highly recommended to add as default since it's crucial for lots of annotation fields.
+**Example**:
+```
+java 
+-Dgenomenexus.enrichment_fields=annotation_summary,my_variant_info 
+-jar annotationPipeline/target/annotationPipeline-*.jar \ -r \ 
+--filename test/data/minimal_example.in.txt \ 
+--output-filename test/data/minimal_example.out.uniprot.txt \ 
+--isoform-override uniprot
+```
+##### Available enrichment fields:
+- annotation_summary:
+    - This field is essential for most annotation processes.
+- my_variant_info
+    - This field provides gnomAD information. Genome Nexus caches static myvariant.info annotation into database.  Upon adding `my_variant_info` to the `enrichment_fields`, Genome Nexus will query the existing variant information from the myvariant.info cache within the database for relevant variants. For new variants, Genome Nexus will retrieve the data from myvariant.info and store it in the database.
+- polyphen
+- sift
+- mutation_assessor
+    - 'mutation_assessor' provides V3 version annotation from Mutation Assessor, which is currently stored in Genome Nexus database
+- nucleotide_context
+- oncokb:
+    - 'oncokb' provides annotations of the biological consequences and clinical implications from OncoKB website. OncoKB token is required (see more information from: [https://www.oncokb.org/apiAccess](https://www.oncokb.org/apiAccess)). Please also provide your token in `-Doncokb.token=abc123` command line parameter, or directly add `oncokb.token=abc123`in the `application.properties`. No OncoKB annotation columns will be added if no valid token is provided
+
 ### Minimal MAF Example
 
 For an example minimal input file see