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src/main/scala/galliaexample/clinvar/ClinvarConstants.scala (6507, 2023-09-20)
src/main/scala/galliaexample/clinvar/ClinvarOriginDecoding.scala (2288, 2023-09-20)
src/main/scala/galliaexample/clinvar/ClinvarVcf.scala (6691, 2023-09-20)
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src/main/scala/galliaexample/vcf/Vcf.scala (1333, 2023-09-20)

__Note__: _This is only intended to showcase processing in Gallia, it is not complete nor thoroughly tested at the moment. Use output at your own risk._ See original announcement on [BioStars](https://www.biostars.org/p/490469/). For more information, see gallia-core [documentation](https://github.com/galliaproject/gallia-core/blob/init/README.md#introducing-gallia-a-scala-library-for-data-manipulation), in particular the bioinformatics examples [section](https://github.com/galliaproject/gallia-core/blob/init/README.md#bioinformatics-examples). ### Description Uses _Gallia_ [transformations](https://github.com/galliaproject/gallia-clinvar/blob/init/src/main/scala/galliaexample/clinvar/ClinvarVcf.scala#L14) to turn VCF rows such as: ```plain #CHROM POS ID REF ALT QUAL FILTER INFO 1 1049066 706774 G A . . AF_EXAC=0.00007;AF_TGP=0.00040;ALLELEID=694996;CLNDISDB=MONDO:MONDO:0014052,MedGen:C3808739,OMIM:615120;CLNDN=Myasthenic_syndrome,_congenital,_8;CLNHGVS=NC_000001.11:g.1049066G>A;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;CLNVC=single_nucleotide_variant;CLNVCSO=SO:0001483;GENEINFO=AGRN:375790;MC=SO:0001627|intron_variant;ORIGIN=1;RS=201995572 ``` into objects like: ```json { "CHROM": "1", "POS": 1049066, "_id": "706774", "REF": "G", "ALT": "A", "clinvar_allele_id": "694996", "HGVS_expression": "NC_000001.11:g.1049066G>A", "variation_review_status": "criteria_provided,_single_submitter", "clinical_significance": "Benign", "allele_origin": [ "germline" ], "disease": [ { "preferred_name": "Myasthenic_syndrome,_congenital,_8", "terms": [ { "database": "MONDO", "id": "MONDO:0014052" }, { "database": "MedGen", "id": "C3808739" }, { "database": "OMIM", "id": "615120" } ] } ], "genes": [ { "symbol": "AGRN", "entrez": "375790" } ], "molecular_consequences": [ { "term": "SO:0001627", "name": "intron_variant" } ], "variant_type": { "name": "single_nucleotide_variant", "term": "SO:0001483" }, "AF": { "EXAC": 0.00007, "1KGP": 0.00040 } } ``` ### Clinvar References - __AMA__: _Landrum MJ, Lee JM, Riley GR, et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014;42(Database issue):D980-D985. doi:10.1093/nar/gkt1113_ - __MLA__: _Landrum, Melissa J et al. “ClinVar: public archive of relationships among sequence variation and human phenotype.” Nucleic acids research vol. 42,Database issue (2014): D980-5. doi:10.1093/nar/gkt1113_ - __APA__: _Landrum, M. J., Lee, J. M., Riley, G. R., Jang, W., Rubinstein, W. S., Church, D. M., & Maglott, D. R. (2014). ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic acids research, 42(Database issue), D980–D985. https://doi.org/10.1093/nar/gkt1113_ - __NLM__: _Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, Maglott DR. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014 Jan;42(Database issue):D980-5. doi: 10.1093/nar/gkt1113. Epub 2013 Nov 14. PMID: 24234437; PMCID: PMC3965032._

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