Script to convert Duplex Sequencing .mutpos file formats into valid VCF files

A python script for generating sample VCF data based on a template VCF

Filter a VCF to discard false positive variants

Snake Genotyping By Sequencing. A reimplementation of Fast-GBS using snakemake.

Shell workflow designed to process Whole Exome Sequencing (WES) data following GATK4 best practices for variant calling.

Variant calling format (vcf) file genomics pipeline for HPC and cloud

A pipeline to study intratumor heterogeneity (ITH) with Canopy

Scripts and containers to run the variant callers originally used in ONCOLINER

Germline variant calling pipeline

Source code to support the paper: "Extensive mitochondrial population structure and haplotype-specific variation in metabolic phenotypes in the Drosophila Genetic Reference Panel"

Small GATK alignment and variant calling pipeline using python

NextFlow pipeline for mitochondria sequence reconstruction

Pipeline for calling and analyzing variants from RNA-Seq data

Workflow for biological validation of germline SNP and indel variant datasets.

Empirical Bayes somatic variant calling

Convert SNVs/InDels from the Human Genome version 19 (hg19) to version 38 (hg38)

Optimized Python and C++ implementations of INDELseek, a Perl tool for detecting complex genetic indels in NGS data, with performance improvements, validation, and benchmarking against other variant callers.

Machine learning pipeline for predicting pathogenicity of somatic variants in cancer genomics using Snakemake and scikit-learn

Variant Calling Snakemake Pipeline

LoFreq nextflow pipeline