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

bowtie2Ultra-fast, sensitive gapped, short-read aligner.
bwaSoftware package for mapping low-divergent sequences against a large reference genome.
StampyA statistical algorithm for sensitive and fast mapping of Illumina sequence reads.
PicardA 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.
GATKGenome Analysis Toolkit, wide variety of tools with a primary focus on variant discovery and genotyping in high-throughput sequencing data.
SAMtoolsVarious utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
VCFtoolsEasily accessible methods for working with complex genetic variation data in the form of VCF files.
FreebayesA Bayesian haplotype-based variant detector.
VarScanPlatform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated from NGS platforms.
PlatypusA haplotype-based variant called for data from NGS platforms.
VarDictA novel and versatile variant caller for next-generation sequencing in cancer research.
SNVerA statistical tool for variant calling in analysis of pooled or individual NGS data.
LoFreqFast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data.
CNVnatorDiscover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
ExomeCNVDetect CNV and LOH from exome sequencing data.
BreakDancerGenome-wide detection of structural variants from next generation paired-end sequencing reads.
Delly2Integrated SV prediction method to discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in next-gen sequencing data.
BreakSeq2A junction-mapping algorithm for rapid and enhanced SV detection and genotyping, estimates zygosity of the calls, supports the SAM/BAM file format.
MantaCall 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.
LumpyA novel and general probabilistic SV discovery framework that naturally integrates multiple SV detection signals.
ANNOVARFast and easy variant annotation, including gene-based, region-based and filter-based annotations on a variant call format (VCF) file generated from human genomes.
VEPDetermines the effect of variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
SnpEffGenomic variant annotation and functional effect prediction toolbox.
SnpSiftAnnotate genomic variants using databases, filters, and manipulates annotated variants.
VarAFTAnnotate and pinpoint human disease-causing mutations through access to multiple layers of information

File types

Group 2983CSV
Group 2994TSV
Group 3005SAM
Group 3016BAM
Group 3027CRAM
Group 3049FASTA
Group 3038FASTQ
Group 3060BED
Group 3071Wig
Group 3082bigBED
Group 3093bigWig
Group 3137bedGraph
Group 3104GTF
Group 3126GFF3
Group 3148VCF

Visual analytics

Pie chartSlice and dice variants based on various features.
Bar chartSlice and dice variants based on various features.
Venn diagramGenerate Venn diagrams of shared variants across cohorts.
HeatmapVisualize SV breakpoints.
Circular plotVisualize balanced SVs, unbalanced SVs and non-canonical complex SVs (cxSVs).
Phylogenetic treeEvolutionary relationships of cultivars or lines mapped to a reference strain.
Genome browserVisualize your alignments and variants overlaid with annotation.