Mapping and variant calling pipeline

Author: Carolina Pita Barros
Contact: carolina.pitabarros@wur.nl
ABG

Path to pipeline: /lustre/nobackup/WUR/ABGC/shared/PIPELINES/mapping-variant-calling

Link to the repository

First follow the instructions here:

Step by step guide on how to use my pipelines
Click here for an introduction to Snakemake

ABOUT

This is a pipeline to map short reads to a reference assembly. It outputs the mapped reads, a qualimap report and does variant calling.

Tools used:

• Bwa-mem2 - mapping
• Samtools - processing
• Qualimap - mapping summary
• Freebayes - variant calling
• Bcftools - VCF statistics

Pipeline workflow

Edit config.yaml with the paths to your files

OUTDIR: /path/to/output 
READS_DIR: /path/to/reads/ # don't add the reads files, just the directory where they are
ASSEMBLY: /path/to/assembly
PREFIX: <output name>

• OUTDIR - directory where snakemake will run and where the results will be written to
• READS_DIR - path to the directory that contains the reads
• ASSEMBLY - path to the assembly file
• PREFIX - prefix for the final mapped reads file

If you want the results to be written to this directory (not to a new directory), comment out

READS_DIR: /path/to/reads/

RESULTS

• dated file with an overview of the files used to run the pipeline (for documentation purposes)
• sorted_reads directory with the file containing the mapped reads
• results directory containing the qualimap results
• variant_calling directory containing the variant calling VCF file and a file with with VCF statistics