06845edb9038bb632170891cebcdc8f477f2ea8d angie Fri Dec 4 08:59:38 2015 -0800 Add dbNSFP v3.1a (including VEST scores) to hg38 for hgVai. Add hgVai options for adding in transcript status info: GENCODE tags when applicable, knownCanonical for knownGene, refSeqStatus for refGene. refs #16502, #16503 diff --git src/hg/lib/dbNsfpVest.as src/hg/lib/dbNsfpVest.as new file mode 100644 index 0000000..809dbf2 --- /dev/null +++ src/hg/lib/dbNsfpVest.as @@ -0,0 +1,19 @@ +table dbNsfpVest +"VEST scores provided by dbNSFP (http://dbnsfp.houstonbioinformatics.org/)" + ( + string chrom; "Reference sequence chromosome or scaffold" + uint chromStart; "Start position in chromosome" + uint chromEnd; "End position in chromosome" + enum('A','C','G','T','.') refAl; "Allele found in reference assembly" + lstring ensTxId; "Ensembl transcript ID(s)" + lstring vestTxId; "ID of transcript on which VEST prediction was made" + enum('A','C','G','T') altAl1; "Alternate allele #1" + lstring var1; "Protein change(s) caused by altAl1" + lstring score1; "VEST score(s) for altAl1, or '.' if n/a" + enum('A','C','G','T') altAl2; "Alternate allele #2" + lstring var2; "Protein change(s) caused by altAl2" + lstring score2; "VEST score(s) for altAl2, or '.' if n/a" + enum('A','C','G','T') altAl3; "Alternate allele #3" + lstring var3; "Protein change(s) caused by altAl3" + lstring score3; "VEST score(s) for altAl3, or '.' if n/a" + )