snakemake-deepvariant

This is sankemake-wrapper of variant calling workflow using DeepVariant.

Authors

yiolino

How to use

Step 1: Obtain a copy of this workflow

• Create a new github repository using this workflow as a template.
• Clone the newly created repository to your local system, into the place where you want to perform the data analysis.

$ git clone https://github.com/tetsuro90/snakemake-deepvariant.git

Step 2: Move your fastq file to snakmake-deepvariant/working/data/reads/

Step 3: Move your fasta file to snakmake-deepvariant/working/data/ref/

Step 4: edit snakmake-deepvariant/working/unit.tsv and snakmake-deepvariant/working/sample.tsv

An example is shown below.

sample	platform	fq1	fq2
SRR1770413	ILLUMINA	data/reads/SRR1770413_1.fastq.gz	data/reads/SRR1770413_2.fastq.gz
SRR341549	ILLUMINA	data/reads/SRR341549_1.fastq.gz	data/reads/SRR341549_2.fastq.gz

sample
SRR1770413
SRR341549

Step 5: run & enter docker container

$ cd snakmake-deepvariant/
$ docker-compose up -d
$ docker exec -it deepvariant /bin/bash

Step 6: run sankemake workflow

$ cd working/
$ snakemake -j {#CORE} --use-conda all

Step 7: make a report html

Once the workflow has been successfully completed, you can output a report file.

$ snakemake --report

License

MIT License

Acknowledgements

• DeepVariant. Copyright 2017 Google LLC. BSD-3-Clause license.
• DeepVariant bioconda package. Copyright 2018 Brad Chapman. MIT license.
• Snakemake workflow: dna-seq-gatk-variant-calling. Copyright 2018, Johannes Köster. MIT license.
• fastp. Copyright 2017 OpenGene - Open Source Genetics Toolbox. MIT license.
• samtools. Copyright 2008-2019 Genome Research Ltd. The MIT/Expat License.
• gatk-lite. Copyright Broad Institue, Inc. MIT license.
• gatk4. Copyright 2009-2020, Broad Institute, Inc. BSD-3-Clause license.
• bwa. Copyright 2009, Li H. and Durbin R. GPLv3 License.