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.
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.
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.
ALoFT provides extensive annotations to putative loss-of-function variants (LoF) in protein-coding genes including functional, evolutionary and network features.
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.
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).
fitCons, the fitness consequences of functional annotation, integrates functional assays (such as ChIP-Seq) with selective pressure inferred using the INSIGHT method.
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.