Introduction

Genomic variant analysis identifies Single Nucleotide Polymorphisms (SNPs) and small Insertions/Deletions (Indels), providing valuable insights into genetic variations that can impact an organism’s traits, diseases, or response to environmental factors.

Workflow

An overview of our genomic variant analysis pipeline is shown below. Key steps include sequence quality evaluation using FastQC, read trimming and filtering using Trimmomatic, decontamination with BBDuk, mapping with BWA-MEM2, and finally additional processing and variant calling with GATK.

The final results of the pipeline are outlined in blue.

1. An HTML formatted sequencing quality report produced by FastQC.
2. A VCF formatted file containing all SNPs prior to any filtration.
3. A VCF formatted file containing all indels prior to any filtration.
4. A VCF formatted file containing all SNPs that passed quality filtration.
5. A VCF formatted file containing all indels that passed quality filtration.
6. A final analysis report in PDF format containing a description of the methods used and some additional QC and summary figures.

Pricing

Our current price for this analysis is $75 per sample.

References

Please refer to these resources and tools that form an integral part of the pipeline process.

1. FastQC – A quality control tool for high throughput sequence data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
2. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014 Aug 1;30(15):2114-20. doi: 10.1093/bioinformatics/btu170
3. BBDuk – Part of the BBTools suite of programs. http://sourceforge.net/projects/bbmap/
4. Vasimuddin Md, Sanchit Misra, Heng Li, Srinivas Aluru. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019. doi: 10.1109/IPDPS.2019.00041
5. Poplin R, Ruano-Rubio V, DePristo MA, Fennell TJ, Carneiro MO, Van der Auwera GA, Kling DE, Gauthier LD, Levy-Moonshine A, Roazen D, Shakir K, Thibault J, Chandran S, Whelan C, Lek M, Gabriel S, Daly MJ, Neale B, MacArthur DG, Banks E. (2017). Scaling accurate genetic variant discovery to tens of thousands of samples bioRxiv, 201178. doi: 10.1101/201178

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