carolinapb/wur_mapping-variant-calling

Short read mapping and variant calling

layout
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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:

• Bwamem2 - mapping
• Samtools - processing
• Qualimap - mapping summary
• Freebayes - variant calling

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), and comment out OUTDIR: /path/to/output in the config file

For the mapping step you should have one _1 fastq file and one _2 fastq file in READS_DIR. If you have several _1 and _2 fastq files from the same sample, you can combine them so you have one file for all _1 reads and one for all the _2 reads. This can be done by concatenating them using cat, if the original files are not compressed (fastq or fq extension), or zcat if the original files are compressed (fastq.gz or fq.gz extension). Example where your files are in the same directory and are compressed:

zcat *_1.fastq.gz > <new file name>_1.fastq.gz
zcat *_2.fastq.gz > <new file name>_2.fastq.gz

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 file with VCF statistics