deepvariant_nf

This repository contains a Nextflow variant calling pipeline for analyzing Next-Generation Sequencing (NGS) data using deepvariant.

%%{init: {'theme':'base'}}%%
flowchart TB
    subgraph "input"
    v0["trimmed reads"]
    v1["reference"]
    v30["indices"]
    v31["vep_DB"]
    end
    subgraph "output"
    v18["vcf"]
    v25["html"]
    end
    v8([ALIGN])
    v9([FLAGSTAT])
    v10([QUALIMAP])
    v13([BAMINDEX])
    v14([VARCALL])
    v17([ANNOTATE])
    v24([REPORT])
    v21(( ))
    v22(( ))
    v23(( ))
    v0 --> v8
    v1 --> v8
    v30 --> v8
    v8 --> v9
    v8 --> v10
    v8 --> v13
    v8 --> v14
    v9 --> v21
    v10 --> v22
    v13 --> v14
    v1 --> v14
    v14 --> v17
    v17 --> v18
    v17 --> v23
    v31 --> v14
    v30 --> v14
    v21 --> v24
    v22 --> v24
    v23 --> v24
    v24 --> v25

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Description

The pipeline is implemented in Nextflow and includes several stages for NGS data analysis:

1. ALIGN: Sequence alignment using BWA mem.
2. FLAGSTAT: Alignment quality control using Samtools flagstat.
3. QUALIMAP: Alignment quality control using Qualimap.
4. FAINDEX: Fai index creation using Samtools faidx.
5. BAMINDEX: Bai index creation using Samtools index.
6. PREPARE: File processing and preparation using Samtools.
7. VARCALL: Variant calling using deepvariant.
8. ANNOTATE: Annotation using VEP (Variant Effect Predictor).
9. REPORT: Compiling report using MultiQC.

Usage

Quick Start

To quickly run the pipeline, use the following command:

nextflow run glebus-sasha/deepvariant_nf \
-profile <docker/singularity> \
--reference <path-to-reference> \
--reads <path-to-reads-folder> \
--outdir results

Requirements

• Nextflow (https://www.nextflow.io/docs/latest/install.html)
• Docker (https://docs.docker.com/engine/install/) or
• Singularity (https://github.com/sylabs/singularity/blob/main/INSTALL.md)

Running the Pipeline

1. Install all the necessary dependencies such as Nextflow, Singularity.
2. Clone this repository: git clone https://github.com/glebus-sasha/deepvariant_nf.git
3. Navigate to the pipeline directory: cd deepvariant_nf
4. Edit the nextflow.config file to set the required parameters, if necessary.
5. Run the pipeline, setting the required parameters, for example:

nextflow run main.nf

License

This project is licensed under the MIT License.