audit_item_status

Ensemble-based approaches (support vector machine) that integrates multiple scoring methods.

External Lab, Community

metasvm

MetaSVM

VARITY is an approach for pathogenicity prediction, which has been specifically optimized for rare missense variation.

varity

VARITY

Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata.

scanpy

Scanpy

Genome-wide single nucleotide variants and short indels effects/prioritization.

Martin Kircher, BIH

cadd

CADD

gMVP is a graph attention neural network model designed to effectively represent or learn the representation of protein sequence and structure context to improve missense variant prediction of disease impact.

gmvp

gMVP

A high-throughput web-server capable of predicting the functional consequences of both coding variants, i.e. non-synonymous single nucleotide variants (nsSNVs), and non-coding variants in the human genome.

fathmm

FATHMM

Jesse Engreitz, Stanford

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

bowtie2

Bowtie 2

Predrag Radivojac, Northeastern

mutpred-lof

MutPred-LOF

Alan Boyle, UMich

surf and turf

SURF and TURF

REVEL is an ensemble method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons.

revel

REVEL

ALoFT provides extensive annotations to putative loss-of-function variants (LoF) in protein-coding genes including functional, evolutionary and network features.

aloft

ALoFT

NumPy is a software enabling numerical computing with Python.

numpy

NumPy

PrimateAI is a deep residual neural network for classifying the pathogenicity of missense mutations.

primateai

PrimateAI

M-CAP is the first pathogenicity classifier for rare missense variants in the human genome that is tuned to the high sensitivity required in the clinic.

m-cap

M-CAP

remm

ReMM

Eigen is a spectral approach to the functional annotation of genetic variants in coding and noncoding regions.

eigen & eigen pc

Eigen & Eigen PC

ClinPred is an efficient tool for identifying disease-relevant nonsynonymous variants.

clinpred

ClinPred

Samtools is a suite of programs for interacting with high-throughput sequencing data. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments (PMID:19505943).

samtools

Samtools

fitCons, the fitness consequences of functional annotation, integrates functional assays (such as ChIP-Seq) with selective pressure inferred using the INSIGHT method.

fitcons

fitCons

A deep neural network (DNN) algorithm for deleterious annotation of genetic variants using neural networks (DANN).

dann

DANN

Zhiping Weng, UMass

zmotif

ZMotif

Jason Ernst, UCLA

drem

DREM

Cell Ranger is a set of analysis pipelines that process Chromium single cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.

Lab

Award