SNP Calling Service

What is SNP Calling?

Genomic variants, including SNPs and indels, are identified through variant analysis pipelines that combine short-read aligners and variant callers. However, the lack of concordance among these pipelines has led to a growing need for standardization and performance benchmarking in the clinical genomics community.

Once the raw sequence reads have been aligned and stored in the SAM/BAM or CRAM file format, the bioinformatics pipeline continues with variant calling. Variant calling involves identifying differences between the aligned reads and the reference genome to detect genetic alterations. SNP calling and CNV calling play a critical role in understanding genetic variations and their impact on various biological processes, disease susceptibility, and personalized medicine.

Our SNP Calling Service

At CD Genomics, we understand the importance of accurate variant calling in genomics research and clinical applications. Our SNP Calling Service combines state-of-the-art algorithms and advanced methodologies to deliver reliable and high-quality results. We employ robust pipelines that integrate short-read aligners and variant callers to identify SNPs with exceptional accuracy.

With our service, you can expect:

• Accurate SNP Identification: Our advanced algorithms leverage cutting-edge techniques to identify SNPs in your genomic data, taking into account factors such as read depth, variant frequency, and statistical confidence.
• Comprehensive Variant Annotation: Once the SNP calls have been meticulously filtered, we proceed to annotate the variants with a wealth of relevant information. Our annotation process encompasses vital aspects such as functional impact, gene associations, population frequencies, and known disease associations. By enriching the identified SNPs with comprehensive annotations, we provide you with invaluable insights into their potential biological significance.
• Stringent Quality Control: To maintain the utmost standards of accuracy and reliability, we subject the SNP calls to rigorous quality control and validation measures. Our extensive validation process includes concordance assessments with known variants, cross-sample or replicate comparisons, and validation against independent datasets, whenever available. This ensures that our SNP calls meet the highest standards of quality and accuracy.
• In-Depth Result Interpretation and Comprehensive Reporting: Finally, we deliver a comprehensive and meticulously prepared report that offers a detailed interpretation of the SNP calling results. The report encompasses a wealth of information, including the genomic coordinates of the identified SNPs, their annotations, quality scores, and any other pertinent metrics. Our team of experts is also available to provide insightful interpretation and consultation to aid in your understanding and effective utilization of the results.
• Customized Analysis: Our team works closely with you to understand your research objectives and specific requirements. We offer tailored analysis approaches and consultation to ensure that our SNP calling service aligns perfectly with your project goals.
• Data Security and Confidentiality: We prioritize the security and confidentiality of your genomic data. Our infrastructure and protocols are designed to protect your sensitive information at all times.

Workflow of SNP Calling

SNP calling (Wang 2016)

How It Works

Throughout the entire process, we prioritize open communication, collaboration, and adherence to professional standards. By utilizing our SNP Calling Service, you can confidently unlock the potential of your genomic data, gain valuable insights into genetic variations, and advance your research in diverse fields such as genetics, genomics, population studies, and personalized medicine.

Reference

1. Wang, Jing. The genomic signatures of adaptive evolution in Populus. Diss. Umeå University, 2016.