ClairS - a deep-learning method for long-read somatic small variant calling

Generic human DNA variant annotation pipeline

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

A collection of Python modules equivalent to R ReQTL Toolkit aims to identify the association between expressed SNVs with their gene expression using RNA-sequencing data.

Filters for Next Generation Sequencing

A collection of software to work with genomic variants

Pipeline to call SNV's with 4 tools (VarDict, LoFreq, Mutect2 & SiNVICT)

A snakemake pipeline that performs variant calling of Nanopore reads from FastQ files for non-model organisms

A somatic mutation signature simulator

Determine read depth and variant frequency thresholds to distinguish NGS sequencing errors from true SNPs. Simulates effect of changing per-site read depth and variant frequency on accuracy of genetic diversity measures (pi, alterante allele frequency, shannon diversity).