Explanation of gavin_r0.5_calibvars.caddannot.clusters.tsv.gz.

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Rows in the data (n = 399,393):
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.

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Columns in the data:
1: GENEONTOL_cluster, a clustering of genes based on Gene Ontology annotations.
2: CADDPATHO_cluster, a clustering of genes based on aggregate CADD properties of pathogenic variants.

Basic variant annotation, this includes gene, group (PATHOGENIC/POPULATION), effect and impact from SnpEff, and CADD scaled score (same as very last column).
3: gene
4: chr
5: pos
6: ref
7: alt
8: group
9: effect
10: impact
11: cadd

All features of CADD annotation.
For full description and to see which are used to train the original CADD scores, see: http://cadd.gs.washington.edu/static/ReleaseNotes_CADD_v1.3.pdf.
12: Chrom
13: Pos
14: Ref
15: Anc
16: Alt
17: Type
18: Length
19: isTv
20: isDerived
21: AnnoType
22: Consequence
23: ConsScore
24: ConsDetail
25: GC
26: CpG
27: mapAbility20bp
28: mapAbility35bp
29: scoreSegDup
30: priPhCons
31: mamPhCons
32: verPhCons
33: priPhyloP
34: mamPhyloP
35: verPhyloP
36: GerpN
37: GerpS
38: GerpRS
39: GerpRSpval
40: bStatistic
41: mutIndex
42: dnaHelT
43: dnaMGW
44: dnaProT
45: dnaRoll
46: mirSVR-Score
47: mirSVR-E
48: mirSVR-Aln
49: targetScan
50: fitCons
51: cHmmTssA
52: cHmmTssAFlnk
53: cHmmTxFlnk
54: cHmmTx
55: cHmmTxWk
56: cHmmEnhG
57: cHmmEnh
58: cHmmZnfRpts
59: cHmmHet
60: cHmmTssBiv
61: cHmmBivFlnk
62: cHmmEnhBiv
63: cHmmReprPC
64: cHmmReprPCWk
65: cHmmQuies
66: EncExp
67: EncH3K27Ac
68: EncH3K4Me1
69: EncH3K4Me3
70: EncNucleo
71: EncOCC
72: EncOCCombPVal
73: EncOCDNasePVal
74: EncOCFairePVal
75: EncOCpolIIPVal
76: EncOCctcfPVal
77: EncOCmycPVal
78: EncOCDNaseSig
79: EncOCFaireSig
80: EncOCpolIISig
81: EncOCctcfSig
82: EncOCmycSig
83: Segway
84: tOverlapMotifs
85: motifDist
86: motifECount
87: motifEName
88: motifEHIPos
89: motifEScoreChng
90: TFBS
91: TFBSPeaks
92: TFBSPeaksMax
93: isKnownVariant
94: ESP_AF
95: ESP_AFR
96: ESP_EUR
97: TG_AF
98: TG_ASN
99: TG_AMR
100: TG_AFR
101: TG_EUR
102: minDistTSS
103: minDistTSE
104: GeneID
105: FeatureID
106: CCDS
107: GeneName
108: cDNApos
109: relcDNApos
110: CDSpos
111: relCDSpos
112: protPos
113: relProtPos
114: Domain
115: Dst2Splice
116: Dst2SplType
117: Exon
118: Intron
119: oAA
120: nAA
121: Grantham
122: PolyPhenCat
123: PolyPhenVal
124: SIFTcat
125: SIFTval

Outcome of CADD model in raw SVM and logarithmically scaled PHRED scores.
126: RawScore
127: PHRED