From: Phenotype-driven strategies for exome prioritization of human Mendelian disease genes
Software | Exome input | Types of variant analyzed | Availability | Software approach |
---|---|---|---|---|
VEP | Various including VCF, pileup, HGVS notations | All | Website, command line and REST service | Filtering by allele frequency and deleteriousness scores (SIFT, PolyPhen) |
ANNOVAR | Various including multi-sample VCF | All | Command line | Filtering by allele frequency, inheritance model and deleteriousness scores (SIFT, PolyPhen, MutationTaster, MutationAssessor, LRT, FATHMM, MetaSVM, MetaLR, GERP++, PhyloP, SiPhy, CADD) |
eXtasy | Single sample VCF | Non-synonymous only | Website and command line | Prioritization based on a Random Forest score from combined deleteriousness scores (CAROL, LRT, MutationTaster, PhastCons, PhyloP, PolyPhen, SIFT), haploinsufficiency, and similarity of the gene to genes annotated with the input Human Phenotype Ontology (HPO) phenotypes as measured by sequence similarity, co-expression, and involvement in the same pathway or protein–protein interactions |
Phevor | Pre-filtered VAAST or ANNOVAR files or functionally annotated multi-sample VCF | All | Website | Prioritization based on semantic similarity of each candidate gene to genes annotated with the input set of ontology terms taken from HPO, Mammalian Phenotype Ontology (MPO), Disease Ontology (DO), and Gene Ontology (GO) |
Phen-Gen | Multi-sample family VCF | All | Website and command line | Filtering by inheritance model and stringency or reentrance. Prioritization based on predicted variant impact and semantic phenotypic similarity between HPO input and HPO-annotated diseases associated with each exomic candidate or its neighbors in an interaction network |
PhenIX | Multi-sample family VCF | All coding | Website and command line | Filtering by allele frequency, variant quality, and inheritance model. Prioritization based on predicted deleteriousness (SIFT, PolyPhen, MutationTaster), allele frequency and semantic phenotypic similarity between HPO input and HPO-annotated diseases associated with each exomic candidate |
Exomiser | Multi-sample family VCF | All coding | Website and command line | Filtering by allele frequency, variant quality, deleteriousness scores and inheritance model. Prioritization based on predicted deleteriousness (SIFT, PolyPhen, MutationTaster), allele frequency and semantic phenotypic similarity between HPO input and HPO-annotated diseases, MPO-annotated mouse and Zebrafish Phenotype Ontology (ZPO)-annotated fish models associated with each exomic candidate or its neighbors in an interaction network |