DNA polymorphism Tools

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

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.

JASMINE (Jointly Accurate Sv Merging with Intersample Network Edges) is an automated pipeline for alignment and SV calling in long-read datasets. The tool is used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine represents the set of all SVs across samples as a network, and uses a modified minimum spanning forest algorithm to determine the best way of merging the variants such that each merged variants represents a set of analogous variants occurring in different samples.

Fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis.

Snpeff is an open source tool that annotates variants and predicts their effects on genes by using an interval forest approach

VarScan, an open source tool for variant detection that is compatible with several short read align-ers.

BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.

cellsnp-lite is an efficient tool for genotyping single cells. cellsnp-lite was initially designed to pileup the expressed alleles in single-cell or bulk RNA-seq data, which can be directly used for donor deconvolution in multiplexed single-cell RNA-seq data, particularly with vireo, which assigns cells to donors and detects doublets, even without genotyping reference. Now besides RNA-seq data, cellsnp-lite could also be applied on DNA-seq and ATAC-seq data, either in bulk or single-cell.

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.

Fast calculation of the ABBA-BABA statistics across many populations/species.

Sequence-graph-based tool to analyze variation in short tandem repeat regions.