gatk-bestpractices
There are 12 repositories under gatk-bestpractices topic.
biowdl/RNA-seq
A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample
ESR-NZ/human_genomics_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.
biowdl/germline-DNA
A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
Sydney-Informatics-Hub/Fastq-to-BAM
Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi
digo4/Clinical-Genomics
Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline
nickhir/GermlineMutationCalling
An adaptable Snakemake workflow which uses GATKs best practice recommendations to perform germline mutation calling starting with BAM files
RhettRautsaw/VariantCaller
VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.
biowdl/gatk-variantcalling
A pipeline that calls variants on a group of BAM files. Category:Multi-Sample
tdayris/fair_gatk_mutect2
Snakemake workflow used to call germline and/or somatic variants with GATK Mutect2
AbdelrahmanYahia/wes_gatk
Whole exome sequencing snakemake workflow based on GATK best practice
laura-budurlean/GATK-WGS-Pipeline
GATK WGS workflow
sbresnahan/TexasCancerGenomics
Analysis of paired tumor-normal whole exome sequencing data generated in a pilot open-access study of participants in Texas.