Exome sequencing Tools

DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file.

Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.

Efficient and comprehensive structural variant caller for massive parallel sequencing data. Identify chromosomal rearrangements using Mate Pair or Paired End sequencing data. It allows identification of intra and inter-chromosomal translocations, deletions, tandem-duplications and inversions, using supplementary alignments as well as discordant pairs.

A rapid, high-throughput, and variant-aware in silico off-target site identification for CRISPR genome editing. Tool package to perform in-silico CRISPR analysis and assessment. CRISPRitz is a software package containing 5 different tools dedicated to perform predictive analysis and result assessement on CRISPR/Cas experiments.