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FAQs

Find quick answers to frequently asked questions about Gencove

Navigating the Gencove Platform

  • Gencove Saas Demo
  • Adding custom configurations to new projects
  • Moving existing samples to another project
  • How to manage user roles and permissions?
  • How to create a new project?
  • How do I set email notifications for my project?
See all 14 articles

General

  • Can Gencove process deep sequencing data?
  • Where is Gencove located?
  • Where do I send my samples for sequencing?
  • How do I download my data?
  • How do I upload FastQ files?
  • Which browser(s) does Gencove support?
See all 12 articles

Gencove Methodologies

  • What is Effective Coverage?
  • What program is used for genotype imputation?
  • How do you impute genotypes when there are no reads at a site?
  • How do you calculate contamination for a sample?
  • Can I get access to the variants called directly from the BAMs before imputation?
  • What does the LOWCONF filter mean for a variant?
See all 8 articles

Understanding My VCF

  • What is the meaning of the FORMAT fields GT:GP:DS:RC:AC in my VCF?
  • What is this * allele in my VCF?
  • What tools can I use to parse these VCFs?
  • Why are there multiple entries for a given chromosome and position in my VCF? Are these duplicate variants?

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