SNP_Pipeline

Pipeline for calling Single Nucleotide Polymorphisms (SNPs). The pipeline is written in bash.

Variant/SNP calling pipeline steps:

1. Align FASTQ reads to a reference genome to create an alignment file - Mapping step
2. Processing the alignment file (file format conversion, sorting, alignment improvement) - Improvement step
3. Calling the variants - Variant Calling step

Pipeline Requirements:

1. bwa for the alignment
2. samtools/HTS package for processing and calling variants
3. GATK for improving the alignment. You must use GATK v3.7.0, available on the Archived version page

Input command line options:

• -a Input reads file – pair 1
• -b Input reads file – pair 2
• -r Reference genome file
• -e Perform read re-alignment
• -o Output VCF file name
• -f Mills file location
• -z Output VCF file should be gunzipped (*.vcf.gz)
• -v Verbose mode; print each instruction/command to tell the user what your script is doing right now
• -i Index your output BAM file (using samtools index)
• -h Print usage information (how to run your script and the arguments it takes in) and exit

Required input files:

1. Input reads file - pair1
2. Input reads file - pair2
3. Reference genome file
4. Mills file

Execution of the bash script:

./snp_pipeline.bash -a <input reads file -pair1> -b <input reads file -pair2> -r -f -o

Output file:

VCF File