snvs

Personal Cancer Genome Reporter (PCGR)

ClairS: a deep-learning method for long-read tumor–normal pair somatic small variant calling

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

Generic human DNA variant annotation pipeline

A collection of software to work with genomic variants

Strelka2 germline and somatic small variant caller

This script analyzes variant call format (VCF) files to identify genetic variants shared across multiple samples. Given a list of VCF paths, it reports variants present in ≥10-100% of samples (10% increments), showing chromosome, position, alleles, sample count, and percentage. Processes genotype data to ensure accurate variant presence detection

SNV calling from single cell sequencing

Filters for Next Generation Sequencing

Nextflow version of SNVPhyl

Pipelines for SNVs and InDels calling (single sample and joint) in WEGS, WGS, and WES using GATK.

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

This repository will house the scripts used to analyze and represent genomic and temperature data for my dissertation.

Microassembly based somatic variant caller for NGS data

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).

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.

Detect and phase minor SNVs from long-read sequencing data

parser para planillas excel, sobre cargado de potenciales casos covid

A somatic mutation signature simulator

A method for variant graph genotyping based on exact alignment of k-mers