An integrated pipeline for detection of de novo and rare inherited mutations from trios-based next-generation sequencing
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DeNovoGear, a tool to detect denovo mutations using sequencing data of related individuals, which can calls denovo SNPs and INDELs in trios and be used to phase denovo mutations using genotype information at neighboring SNP sites.


PolyMutt uses a likelihood-based framework to call SNVs and detect de novo point mutation in families from next-sequencing data.


DNMFilter is a machine learning based tool designed to filter out false positive de novo mutations (DNMs) obtained by any computational or manual approaches from next generation sequencing data. It can be used as either a stand-alone tool to detect DNM or coupled with other commonly used DNM detection tool (GATK UnifiledGenotyper, polymutt, DenovoGear et al.) to improve specificity.


VarScan is designed to identify SNPs and indels in massively parallel sequencing of single or pooled samples, independent of platform and technology. For single sample, it realizes identification and filtration of germline variants based on read counts, base quality and allele frequency. Somatic status of each variant could also be determined from given data for a tumor-normal pair by comparing read counts of the two.


The program is based on a LD-aware method to infer genotypes and phasing for sequencing in trios (or mixed with undrelated individuals).


FamSeq utilize available information from all family members to more accurately identify new germline mutations, by providing the probability of an individual carrying a variant given the entire family's raw measurements.


MendelScan is a tool developed for mapping linkages for family exome sequencing, scoring and prioritizing candidate variants in family-based studies of inherited disease.


TrioVis is a visual analytics tool developed for filtering on coverage and variant frequency for genomic variants from exome sequencing of parent-child trios.


VAR-MD is a software tool for analyzing the DNA sequence variants produced by human ES. VAR-MD generates a ranked list of variants using predicted pathogenicity, Mendelian inheritance models, genotype quality, and population variant frequency data. VAR-MD has the potential to enhance mutation identification using family based, annotated next generation sequencing data.


Exomiser can functionally annotates variants from whole-exome sequencing data starting from a VCF file (version 4).


ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others).


TADA(Transmission And De novo Association Test) is a novel statistical method that utilizes inherited variation transmitted to affected offspring in conjunction with (de novo) mutations to identify risk genes.


FunSeq used to automatically score and annotate disease-causing potential of SNVs, particularly the non-coding ones.


GATK, defined as Genome Analysis Toolkit, is a software package designed to analyse next-generation resequencing data, which primarily focuses on variant discovery and genotyping. Its sophisticated structure, overwhelmingly processing and computing capacity enables it to undertake large scale projects with assured data quality.


SAMtools is a set of toolkits to efficiently manipulating short DNA sequence read alignments in SAM/BAM format, which also can be used for SNV/InDel calling by offering the so-called mpileup command.


VCFtools offers a software suite to implement functions to validate, merge and compare VCF files which are a kind of format storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants with rich annotations combined. VCFtools also provides a general Perl API.


Bowtie, excels in short read aligning,at a rate of over 25 million 35-bp reads per hour.The memory-efficiency comes from indexing the genome with a Burrow-Wheeler index to keep its memory footprint small.


BWA (Burrows-Wheeler Aligner), a software package adopting three algorithms: BWA-backtrack, BWA-SW and BWA-MEM, is developed for mapping low-divergent sequences against a large reference genome (e.g.human genome). It outperforms many other aligners in processing speed while requires large memory.


SOAPaligner, designed for short oligonucleotide alignment,is updated as a super fast and accurate aligner for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer.


SOAPsnp uses a method based on BAyes' theorem to call consensus genotype by carefully considering the data quality, alignment, and recuring experimental errors. In the first Asian genome re-sequencing project, evaluation of SOAPsnp result on Illumina HapMap 1M BeadChip Duo genotyping sites shows great accuracy. Over 99% of the genotyping sites are covered at over 99.9% consistency.


HugeSeq, an automated pipeline for detecting genetic variants from High-throughput genome sequencing, is a fully integrated system for genome analysis from mapping reads to the identification and annotation of all types of variants: SNPs, InDels and SVs.


SNPTools is not only a SNP caller with high sensitivity and accuracy, but also a suite of tools for highly accurate genotype calling utilizing a novel imputation engine.


SNVMix is a post-alignment tool detecting SNV from NGS data. It calculates the probability of three possible genotypes for each position: aa(homozygous for the reference allele, where the reference is the genome the reads were aligned to), ab (heterozygous) and bb (homozygous for a non-reference allele).


LoFreq infers single-nucleotide variants (SNVs) from high-throughput sequencing data featuring fast speed and high sensitivity.


CoNAn-SNV provides a probabilistic framework for the discovery of single nucleotide variants.


Platypus is a tool which sensitively and specifically detects variant in high-throughput sequencing data by local realigning and assembling of reads.


GAMES identifies and annotates mutations in NGS projects.


This interactive tool allows finding genes affected by deleterious variants that segregate along family pedigrees , case-controls or sporadic samples.


The Human Gene Mutation Database (HGMD) represents an attempt to collate known (published) gene lesions responsible for human inherited disease.


MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.


Online Mendelian Inheritance in Man (OMIM) is a comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily.


All cancers arise as a result of the acquisition of a series of fixed DNA sequence abnormalities, mutations, many of which ultimately confer a growth advantage upon the cells in which they have occurred. There is a vast amount of information available in the published scientific literature about these changes. COSMIC is designed to store and display somatic mutation information and related details and contains information relating to human cancers.


ClinVar provides a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence.


QualitySNPng detects and visualizes SNP from NGS (Next Generation Sequencing) data by using a haplotype-based strategy (applicable on polyploidy species), free from the prerequisite for a fully sequenced reference genome.


BEAGLE performs a series of functionalities for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples: inferring haplotypes and sporadic missing genotype data, imputing ungenotyped markers that have been genotyped in a reference panel and performing single marker and haplotypic association analysis, etc.


vipR is designed to screen for sequence variants (SNPs, deletions) for NGS data.


MACH, based on a Markov Chain, performs genotype phasing and resolves long haplotypes and infer missing genotypes in samples of unrelated individuals.


SolSNP, a java-based DNA variant calling tool for NGS alignment data, deploys a modified Kolmogorov-Smirnov statistic and data filtering to improve the confidence and speed of variant calling on high-coverage aligned genomes.


IMPUTE2 is developed for phasing observed genotypes and imputing missing genotypes.

Copyright©2014, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.