Question: Next-Generation Sequecing And Quantitative Traits Association Study
gravatar for sorento7
6.1 years ago by
sorento730 wrote:

The collaborators have provided me with whole-genome sequencing (30x) called SNPs of ~800 human subjects, processed with a recent version of illumina CASAVA. The SNP markers in VCF posses these quality scores: QUAL, GQ and read depth. I would like to bring these variants to a downstream association study with quantitative traits, using an additive allelic model. Since selecting different thresholds for filtering markers based on QUAL/GQ and Depth will lead to a variable loss of genotype calls especially for low coverage heterozygote markers, and in the other hand, miscalling the heterozygotes (REF/ALT) as ALT/ALT will ONLY impact the beta estimates (not the p-value), what would be a justified filtering strategy?

EDIT: The only paper I have found so far which has exploited NGS in a quantitative-traits association pipeline is this; does there exist anything more? link

variant-calling ngs sequencing • 1.7k views
ADD COMMENTlink modified 3.2 years ago by Biostar ♦♦ 20 • written 6.1 years ago by sorento730
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 802 users visited in the last hour