Variant Discovery

With rapidly falling sequencing costs, whole-exome sequencing (WES) and whole-genome sequencing (WGS) using NGS technologies have become de facto standards to characterize individual genomic landscapes to identify causal genomic variants relevant for understanding disease mechanisms, diagnosis and therapy.

Understand the role of genetic variation in human disease, ancestry, and evolution using community standard GATK-based best practices workflows, or your aligner and variant caller of choice for analyzing Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS) data. Our intelligent execution engine can handle any number of samples, as it automatically parallelizes jobs and minimizes IO. Our workflows can capture both large and small variants, indels, copy number changes, and large structural variants and help you identify potential causative variants for further analysis.

Use popular tools like ANNOVAR, VEP, VarAFT, SnpEff, etc for variant annotation. Upload your VCF files, annotate and filter your variants with gene and transcript features, functional information, allele frequency, evolutionary features, etc. Integrate your results with curated resources like Online Mendelian Inheritance in Man (OMIM), Human Phenotype Ontology (HPO), catalog of cancer-specific databases like COSMIC, CIViC, ClinVar, cBioPortal, NCI Genomic Data Commons, etc.

Overlay filtered variants with other omics datasets, namely, expression (coding and non-coding genes), epigenomics (methylation, histone modifications), chromatin accessibility, etc and visualize using our genome browser.

Tools

Bowtie2	Ultra-fast, sensitive gapped, short-read aligner.
BWA	Software package for mapping low-divergent sequences against a large reference genome.
Stampy	A statistical algorithm for sensitive and fast mapping of Illumina sequence reads.
Picard	A set of Java command line tools for manipulating high-throughput sequencing data in various formats such as such as FASTQ, SAM, BAM, CRAM and VCF.
GATK	Genome Analysis Toolkit, wide variety of tools with a primary focus on variant discovery and genotyping in high-throughput sequencing data.
SAMtools	Various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
VCFtools	Easily accessible methods for working with complex genetic variation data in the form of VCF files.
Freebayes	A Bayesian haplotype-based variant detector.
VarScan	Platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated from NGS platforms.
Platypus	A haplotype-based variant called for data from NGS platforms.
VarDict	A novel and versatile variant caller for next-generation sequencing in cancer research.
SNVer	A statistical tool for variant calling in analysis of pooled or individual NGS data.
LoFreq	Fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data.
CNVnator	Discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
ExomeCNV	Detect CNV and LOH from exome sequencing data.
BreakDancer	Genome-wide detection of structural variants from next generation paired-end sequencing reads.
Delly2	Integrated SV prediction method to discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in next-gen sequencing data.
BreaksSeq2	A junction-mapping algorithm for rapid and enhanced SV detection and genotyping, estimates zygosity of the calls, supports the SAM/BAM file format.
Manta	Call SVs and indels from mapped paired-end sequencing reads, optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
Lumpy	A novel and general probabilistic SV discovery framework that naturally integrates multiple SV detection signals.
ANNOVAR	Fast and easy variant annotation, including gene-based, region-based and filter-based annotations on a variant call format (VCF) file generated from human genomes.
VEP	Determines the effect of variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
SnpEff	Genomic variant annotation and functional effect prediction toolbox.
SnpSift	Annotate genomic variants using databases, filters, and manipulates annotated variants.
VarAFT	Annotate and pinpoint human disease-causing mutations through access to multiple layers of information