Snakemake workflow used to call germline variants with GATK-Mutect2

Usage

The usage of this workflow is described in the Snakemake workflow catalog it is also available locally on a single page.

Results

A complete description of the results can be found here in workflow reports.

Material and Methods

The tools used in this pipeline are described here textually. Web-links are available below:

Index and genome sequences with fair_genome_indexer

See fair_genome_indexer for information about sequences and annotation retrieval.

Raw-sequences QC with fair_fastqc_multiqc

See fair_fastqc_multiqc documentation about ranw sequences quality controls

Bowtie2 Mapping with fair_bowtie2_mapping

See fair_bowtie2_mapping for informatin about sequence alignment and quality controls.

Call variants with Mutect2

Actual Calling

Step	Meta-Wrapper	Wrapper
Per-sample annotation	GATK short variant calling	add-or-replace-groups
Mutect2 calling	GATK short variant calling	mutect2
Infer contaminations	GATK short variant calling	get-pileup-summaries
Estimate corss-sample contamination	GATK short variant calling	calculate-contamination
Search for sequencing artifact bias	GATK short variant calling	learn-read-orientation-model
Filtering calls	GATK short variant calling	filter-mutect-calls

┌─────────────────────────┐           ┌──────────────────────────────┐   
│Annotate samples (Picard)│           │Index annotated bam (Sambamba)│   
└─────────────┬───────────┘           └──────┬───────────────────────┘   
              │                              │                           
              ├──────────────────────────────┘                           
              │                                                          
┌─────────────▼─────────┐                                                
│Call variants (Mutect2)├──────────────────────┐                         
└─────────────┬─────────┘                      │                         
              │                                │                         
              │                                │                         
              │                                │                         
┌─────────────▼────────────┐         ┌─────────▼────────────────────────┐
│Infer contamination (GATK)│         │Estimate sequencing bias artifacts│
└─────────────┬────────────┘         │             (GATK)               │
              │                      └────────────┬─────────────────────┘
              │                                   │                      
┌─────────────▼─────────────────────┐             │                      
│Estimate cross-sample contamination│             │                      
│          (GATK)                   │             │                      
└─────────────────────────────────┬─┘             │                      
                                  │               │                      
                                  ├───────────────┘                      
                                  │                                      
                      ┌───────────▼──────────────────┐                   
                      │Hard filtering variants (GATK)│                   
                      └──────────────────────────────┘                   

Annotate variants of confidence

┌──────────────────────────┐     
│Annotate variants (SnpEff)│     
└──────────────┬───────────┘     
               │                 
               │                 
               │                 
┌──────────────▼────────────────┐
│Annotate variant type (SnpSift)│
└───────────────────────────────┘

Quality controls

Step	Wrapper
Variant Evaluation	variant-eval
MultiQC	multiqc-wrapper

┌───────────────────────────┐ ┌───────────────────┐ ┌────────────────────┐
│Variant annotation (SnpEff)│ │fair_fastqc_multiqc│ │fair_bowtie2_mapping│
└─────────────────────┬─────┘ └───┬───────────────┘ └───┬────────────────┘
                      │           │                     │                 
                      │           │                     │                 
                      └───────────┼─────────────────────┘                 
                                  │                                       
                                  │                                       
                     ┌────────────▼───────────────┐                       
                     │Report aggregation (MultiQC)│                       
                     └────────────────────────────┘