Copy number variation annotation software tools | Whole-genome sequencing data analysis
Data analysis of CNVs is an important downstream task to mine the biological meaning of resultant CNV lists from large scale genomic experiments. The analysis of such high complexity and large volume data sets is challenging and requires support from specialized bioinformatics software packages.
An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others). Using a desktop computer, ANNOVAR requires ∼4 min to perform gene-based annotation and ∼15 min to perform variants reduction on 4.7 million variants, making it practical to handle hundreds of human genomes in a day.
Determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Simply input the coordinates of your variants and the nucleotide changes to find out the genes and transcripts affected by the variants, location of the variants (e.g. upstream of a transcript, in coding sequence, in non-coding RNA, in regulatory regions), consequence of your variants on the protein sequence (e.g. stop gained, missense, stop lost, frameshift); known variants that match yours, and associated minor allele frequencies from the 1000 Genomes Project, SIFT and PolyPhen scores for changes to protein sequence.
Detects copy number variations (CNVs) with high resolution. PennCNV is an integrated hidden Markov model (HMM) method that incorporates the population allele frequency for each single nucleotide polymorphism (SNP) and the distance between adjacent SNPs. This application was developed specifically for data generated on the Illumina Infinium platform, but it can be extended to other similar SNP genotyping platforms.
Aims to facilitate web-based personal genome annotation. wANNOVAR is a web application that uses ANNOVAR as the backend annotation engine. Users need to submit a list of variants, and the server can process the submission and generate HTML-based result pages. It also allows flexibility by permitting the users to select customized filtering criteria and identify a subset of prioritized variants from thousands or even millions of input variants.
A free web-based phenotype-dependent NGS variant prioritizer, which leverages the wealth of information in GeneCards and its affiliated databases. VarElect employs GeneCards’ powerful search and scoring capacities, and its algorithm affords inferring direct as well as indirect links between sequenced genes and disease/symptom/phenotype keywords. The indirect links benefit from GeneCards’ excellent capacity to relate genes to each other via numerous annotations. VarElect thus provides a robust facility for ranking genes and pointing out their likelihood to be related to a patient’s disease.
Assists users in the annotation of multiple types of human genomic variants in a high-throughput setting. AnnTools is an integrative approach not limited by the specific type or genomic location of the variant, the ability to evaluate both functional and regulatory regions and incorporation of variant frequency data to highlight potentially significant variants. This application allows individual and batch query processing and offers flexibility in input data formats.
Aims to fill the gap between copy number variant detection and interpretation by performing in-depth annotations and functional predictions for copy number variants. SG-ADVISER CNV is designed to allow users with no prior bioinformatics expertise to manipulate large volumes of copy-number variant data.