So why isn’t everyone doing low-pass sequencing and imputation for genotyping and GWAS?
The critical components of low-pass as a solution are 1) access to sequencing, 2) an understanding of the genetic variants in your population, and 3) statistical tools to impute genotypes based on the population knowledge. While generating sequencing data is becoming easier and less expensive over time, the other two take a bit of specialized knowledge. Building a reference panel for a population of interest and using mostly command-line tools to leverage that panel for imputation may not be skills readily available to researchers considering implementing low-pass.
That’s where Gencove comes in. As experts in genetics, low-pass sequencing, and imputation software, we provide an easy-to-use platform to house, analyze, and interpret low-pass sequencing data. Most projects can start right away on the platform, with reference panels for many species available now. For less common species or proprietary populations, tailored panels can be developed with the Gencove team of experts to ensure you’re maximizing the value of your data in the long term.
Once we’ve obtained your FASTQ files of low-pass sequencing data, you can access:
A suite of quality control measures to ensure confidence in your sequencing data
Genotypes for millions of genetic variants from your selected imputation reference panel
Sequence alignments against the reference genome in a portable format
Ancestry estimates from a set of 26 reference populations in human samples
Polygenic risk score estimates for CAD, breast cancer, and prostate cancer in human samples