Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Variant Calling Pipeline Using GATK4 and Nextflow

Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline

gatk4 RNA variant calling pipeline

A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample

A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample

Sentieon DNAseq

An adaptable Snakemake workflow which uses GATKs best practice recommendations to perform germline mutation calling starting with BAM files

GATK 4 Mutect2 Somático

An interactive visualization tool for GATK CNV analysis. Displays modeled segments and raw read/allele counts.

A Snakemake workflow for variant calling using GATK4 best practices

Snakemake based workflow for calling Variants on RNA-Seq data in a joint calling mode

Snakemake pipeline for variant calling using GATK

A pipeline for mitochondrial mutation calling

Steps that I followed setting up Windows Subsystem for Linux 2 (WSL2) and Docker to run NGS data analysis using GATK.

Germline Variant Calling Pipeline built in Snakemake

This a snakemake pipeline to detect Somatic mutations (GATK4 and Mutect2)

Beginner's tutorial for GATK4 workflow on variant calling from RNA-seq.