Explanation of gavin_r0.5_calibvars.cadd_v1.4annot.tsv.gz.

####

Rows in the data (n = 399,518):
Each row represents one genetic variant (mutation) that has been classified as either PATHOGENIC or POPULATION.
The PATHOGENIC variants are considered to be disease causing by reputable sources.
For POPULATION variants this has not been established and are thus presumed to be safe/benign.
The POPULATION variants are selected based on gene-specific properties using the GAVIN method (see: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1141-7) and serve as a highly representative set of negatives.

####

Basic variant annotation, this includes gene, group (PATHOGENIC/POPULATION), effect and impact from SnpEff, and CADD scaled score.
Position (chrom/pos/ref/alt) should be the same as CADD annotation unless something went wrong. Column 9 is equal to CADD PHRED in column 116.
1: gene
2: chr
3: pos
4: ref
5: alt
6: group
7: effect
8: impact
9: cadd

All features for the CADD 1.4 annotation.
For full description and to see which are used to train the original CADD scores, see: https://cadd.gs.washington.edu/static/ReleaseNotes_CADD_v1.4.pdf
10: CaddChrom
11: CaddPos
12: CaddRef
13: CaddAlt
14: Type
15: Length
16: AnnoType
17: Consequence
18: ConsScore
19: ConsDetail
20: GC
21: CpG
22: motifECount
23: motifEName
24: motifEHIPos
25: motifEScoreChng
26: oAA
27: nAA
28: GeneID
29: FeatureID
30: GeneName
31: CCDS
32: Intron
33: Exon
34: cDNApos
35: relcDNApos
36: CDSpos
37: relCDSpos
38: protPos
39: relProtPos
40: Domain
41: Dst2Splice
42: Dst2SplType
43: minDistTSS
44: minDistTSE
45: SIFTcat
46: SIFTval
47: PolyPhenCat
48: PolyPhenVal
49: priPhCons
50: mamPhCons
51: verPhCons
52: priPhyloP
53: mamPhyloP
54: verPhyloP
55: bStatistic
56: targetScan
57: mirSVR-Score
58: mirSVR-E
59: mirSVR-Aln
60: cHmmTssA
61: cHmmTssAFlnk
62: cHmmTxFlnk
63: cHmmTx
64: cHmmTxWk
65: cHmmEnhG
66: cHmmEnh
67: cHmmZnfRpts
68: cHmmHet
69: cHmmTssBiv
70: cHmmBivFlnk
71: cHmmEnhBiv
72: cHmmReprPC
73: cHmmReprPCWk
74: cHmmQuies
75: GerpRS
76: GerpRSpval
77: GerpN
78: GerpS
79: TFBS
80: TFBSPeaks
81: TFBSPeaksMax
82: tOverlapMotifs
83: motifDist
84: Segway
85: EncH3K27Ac
86: EncH3K4Me1
87: EncH3K4Me3
88: EncExp
89: EncNucleo
90: EncOCC
91: EncOCCombPVal
92: EncOCDNasePVal
93: EncOCFairePVal
94: EncOCpolIIPVal
95: EncOCctcfPVal
96: EncOCmycPVal
97: EncOCDNaseSig
98: EncOCFaireSig
99: EncOCpolIISig
100: EncOCctcfSig
101: EncOCmycSig
102: Grantham
103: Dist2Mutation
104: Freq100bp
105: Rare100bp
106: Sngl100bp
107: Freq1000bp
108: Rare1000bp
109: Sngl1000bp
110: Freq10000bp
111: Rare10000bp
112: Sngl10000bp
113: dbscSNV-ada_score
114: dbscSNV-rf_score

Outcome of CADD model in raw SVM and logarithmically scaled PHRED scores.
115: RawScore
116: PHRED