The SNP discovery pipeline is used to detect variants including SNPs and indels (insertion/deletions) from next-generation sequencing (NGS) reads. The pipeline includes the following:
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Alignment: The sequence reads are aligned to the reference genome using BWA (Burrows-Wheeler Aligner) – bwa 0.7.10 http://bio-bwa.sourceforge.net/
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BAM Processing: A series of intermediate steps to process and prepare the BAM file for variant calling. Picard Tools is used for BAM processing – Picard Tools 1.119 http://broadinstitute.github.io/picard/
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Variant calling: Variants are called using the GATK Unified Genotyper – GATK 3.2-2 https://www.broadinstitute.org/gatk/
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FastQC (v.0.11.5): A simple tool that provides an overview of raw data sequence - https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Note in FastQC: if the program failed to export results, the module has an error. Therefore, you need to download the tool.
The pipeline is intended to work on High-Performance Computing (HPC) clusters that has SLURM as a job scheduler. However, the individual python scripts can also be used for specific steps independently.
- Clone repository on your working directory.
- Modify config file accordingly. The config file contains parameters for the directories, software and user information required to run the pipeline.
- Run createInput.py to create input.info file which contains information for the genomes/lines and the number of fastq files for each genome.
- Run snp.sh to submit jobs that will run the pipeline.
- Run log.sh to check for error report.
To see the specific commands, go to https://github.com/InternationalRiceResearchInstitute/variant-calling-pipeline/wiki/How-to-run-the-pipeline.