Snakemake workflow: NCF1_variant_calling

This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.

This workflow is adapted from this Snakemake pipeline: https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling

Many updates were made to the pipeline for calling variants in duplicated regions, like the NCF1 gene.

Authors

• Eric Karlins

Usage

You'll first need to create a fasta file with duplicated regions that match your region of interest masked with Ns.

Step 1: Create masked reference fasta file

1. For NCF1, using the hg38 reference fasta, I created a bed file with two lines to mask the regions of NCF1b and NCF1c. This bed file can be found in resources/NCF1_region_to_mask.bed

2. Next I used bedtools maskfasta to create the masked reference file. The command was:

bedtools maskfasta -fi Homo_sapiens_assembly38_plus.fasta -bed NCF1_region_to_mask.bed -fo Homo_sapiens_assembly38_plus_NCF1_mask.fasta

3. Create the bwa index files for your new fasta reference:

bwa index Homo_sapiens_assembly38_plus_NCF1_mask.fasta

Step 2: Obtain a copy of this workflow

Clone the newly created repository to your local system, into the place where you want to perform the data analysis.

Step 3: Configure workflow

Configure the workflow according to your needs via editing the file config.yaml.

Step 4: Execute workflow

Test your configuration by performing a dry-run via

snakemake --use-conda -n

Execute the workflow locally via

snakemake --use-conda --cores $N

using $N cores or run it in a cluster environment via

snakemake --use-conda --cluster qsub --jobs 100

or

snakemake --use-conda --drmaa --jobs 100

If you not only want to fix the software stack but also the underlying OS, use

snakemake --use-conda --use-singularity

in combination with any of the modes above. See the Snakemake documentation for further details.