define a list of glioma genes and associated variants

[fpbarthel]

@moskalika @Kcjohnson please advise. Currently using this list of glioma genes. See comment for description.

/*
3. Select a list of genes and specific variants
    - Take genes deemed significant using the dNdS-CV method
    - Manually adding genes that are not significant by dNdS but are known glioma genes (handpicked from Anzhela's list)
    - Filter the list of variants by subsetting hotspot variants only for those genes where they are known
*/
SELECT sn.gene_symbol, chrom, pos, alt
    FROM analysis.snvs sn
    INNER JOIN analysis.dndscv_gene ds ON ds.gene_symbol = sn.gene_symbol AND (ds.qglobal_cv < 0.10 OR ds.gene_symbol IN ('TERT','IDH2','NOTCH1','PDGFRA','PIK3CG','BRAF','H3F3A'))
    LEFT JOIN analysis.variant_classifications vc ON sn.variant_classification = vc.variant_classification
    WHERE
        (sn.gene_symbol NOT IN ('TERT','IDH1','IDH2','BRAF','H3F3A') AND variant_classification_priority IS NOT NULL) OR 
        (sn.gene_symbol = 'TERT' AND sn.variant_classification = '5''Flank' AND lower(sn.pos) IN (1295228,1295250)) OR
        (sn.gene_symbol = 'IDH1' AND sn.hgvs_p IN ('p.R132C','p.R132G','p.R132H','p.R132S')) OR
        (sn.gene_symbol = 'IDH2' AND sn.hgvs_p = 'p.R172K') OR
        (sn.gene_symbol = 'BRAF' AND sn.hgvs_p = 'p.V600E') OR
        (sn.gene_symbol = 'H3F3A' AND sn.hgvs_p = 'p.G35R')

[fpbarthel]

You may ask why filter hotspot variants? Well it helps prioritize those variants when multiple exonic variants per gene are found, also it helps remove uninteresting variants eg. in hypermutant tumors.

[fpbarthel]

This is done