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

Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi

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

Whole exome sequencing snakemake workflow based on GATK best practice

VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.

A pipeline that calls variants on a group of BAM files. Category:Multi-Sample

GATK WGS workflow

Snakemake workflow used to call germline and/or somatic variants with GATK Mutect2

Implemented a Bash-based pipeline for human genome variant analysis using pre-aligned NA12878 data, performing duplicate marking, base recalibration, variant calling, filtration, and annotation with Funcotator. Followed GATK Best Practices to obtain high-confidence SNP and INDEL variants.