SNP Variant Calling Pipeline

Customizing scripts

BWA - Burrows Wheeler Aligner

Basic script to perform mapping

bwa mem sample.fasta read1.fastq read2.fastq > output.sam

Modify script to add a parameter for threads

bwa -t 10 mem sample.fasta read1.fastq read2.fastq > output.sam

BWA mem with mismatch penalty

bwa -t 10 -B 6 mem sample.fasta read1.fastq read2.fastq > output.sam

Instructions to run the pipeline through shell script

1. Clone the git repository using the command below. A folder named SNP will be in your current working directory.

   git clone https://gitlab.com/Niranjanpandeshwar/snp

2. Change directory into snp folder

   cd snp

3. Run the “ll” command to see all the files and folders. You should see 3 folders named “input”, “reference” and “output”, a file named snp_script.sh and a Readme.md file. The input folder has some test fastq files. reference folder has a test fasta reference file. The output folder has the expected files.

   ll

4. Run the script with the command below

   ./snp_script.sh -r reference/wildtype.fna -t p -p 2 -i input -o output

5. All files in the input folder will be processed. The output is available in output folder.

   cd output