Skip to main content

Advertisement

Table 1 Comparison of exome analysis tools

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
  1. Abbreviations: CADD Combined Annotation-Dependent Depletion, GERP Genomic Evolutionary Rate Profiling, HGVS Human Genome Variation Society, HPO Human Phenotype Ontology, LRT likelihood ratio test (LRT), PolyPhen Polymorphism Phenotyping, REST Representational State Transfer, SIFT Sorting Intolerant from Tolerant, VAAST Variant Annotation, Analysis, Search Tool, VCF variant call format