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. For more information, see gallia-core documentation, in particular the bioinformatics examples section.
Uses Gallia transformations
to turn VCF rows such as:
#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:
{
"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 }
}- 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.