GATK WGS workflow
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Updated
Jun 12, 2023 - Shell
GATK WGS workflow
Analysis of paired tumor-normal whole exome sequencing data generated in a pilot open-access study of participants in Texas.
Whole exome sequencing snakemake workflow based on GATK best practice
Snakemake workflow used to call germline and/or somatic variants with GATK Mutect2
A pipeline that calls variants on a group of BAM files. Category:Multi-Sample
VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.
An adaptable Snakemake workflow which uses GATKs best practice recommendations to perform germline mutation calling starting with BAM files
Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline
Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi
A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
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
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