ALoFT

Açıklama

datasource: v4.1a
description: ALoFT provides extensive annotations to putative loss-of-function variants (LoF) in protein-coding genes including functional, evolutionary and network features.
developer:
name: ‘Gerstein Lab’
organization: ‘Yale University’
email: ‘support@cravat.us’
website: ‘http://aloft.gersteinlab.org/’
citation: ‘Suganthi Balasubramanian, Yao Fu, Mayur Pawashe, Patrick McGillivray, Mike Jin, Jeremy Liu, Konrad J. Karczewski, Daniel G. MacArthur, and Mark Gerstein. “Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes.” Nature Communications 8 (2017).’
output_columns:
– name: transcript
title: Transcript ID
type: string
width: 70
desc: Ensembl transcript ids
hidden: true
– name: affect
title: Transcripts Affected
type: string
width: 75
desc: the fraction of the transcripts of the gene affected i.e. No. of transcripts affected by the SNP/Total no. of protein_coding transcripts for the gene.
hidden: true
category: multi
– name: tolerant
title: Tolerant Probability
type: float
width: 75
desc: Probability of the SNP being classified as benign by ALoFT
hidden: true
– name: recessive
title: Recessive Probability
type: float
width: 75
desc: Probability of the SNP being classified as recessive disease-causing by ALoFT
hidden: true
– name: dominant
title: Dominant Probability
type: float
width: 75
desc: Probability of the SNP being classified as dominant disease-causing by ALoFT
hidden: false
– name: pred
title: Classification
type: string
width: 85
desc: final classification predicted by ALoFT; values can be Tolerant, Recessive or Dominant
category: multi
hidden: false
– name: conf
title: Confidence
type: string
width: 75
desc: Confidence level of Aloft_pred; values can be “High Confidence” (p < 0.05) or "Low Confidence" (p > 0.05)
category: multi
hidden: true
– hidden: true
name: all
title: All Annotations
type: string
width: 75
filterable: false
table: true
table_headers:
– name: transcript
title: Transcript
type: string
– name: affect
title: Affect
type: string
– name: tolerant
title: Tolerant
type: float
– name: recesive
title: Recessive
type: float
– name: dominant
title: Dominant
type: float
– name: pred
title: Prediction
type: string
– name: conf
title: Confidence
type: string

tags:
– variants
– variant effect prediction

requires_opencravat: ‘>=2.2.1’
requires:
– wgaloft
title: ALoFT
version: 1.0.0
type: annotator
level: variant