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)│ └────────────────────────────┘