Frequently asked questions

• Access and login:
  • Can I register my colleague for data access?
  • Someone I know is a member of the Research Network, but they haven't received login details yet - why?
• Data:
  • How do I identify compound heterozygous mutations within the Genomics England Dataset?
  • How often are the data updated?
  • What is Rare Disease Tiering data?
  • Where can I find information on de novo variants?
  • Why can't I see all the genomes in the 'genomes/by_date' folder?
  • Why do some participants have multiple genomic data on the same reference assembly?
  • How do I know if a pathogenic variant with a high allele frequency is true or a variant calling error?
• Tools:
  • Can I bring in docker/container?
  • Can I install software in the Research Environment?
  • Cytoscape, How to start it up?
  • Cytoscape, How to use the API with R?
  • Is it possible to annotate variants within the Research Environment?
  • Is there an R package we can use to interrogate data from LabKey?
  • Problem loading IGV in the research environment
  • Vcf2maf on the HPC
  • Which version of BCFtools 1.10.2 should I use on the HPC?
  • LabKey curl_fetch_memory error
  • LabKey DOCTYPE error
  • libfortran errors when loading packages in R
  • Loading R packages when versions are not synchronised
  • Rpackage "CURL_OPENSSL_3" not found
• Research:
  • Creating "lollipops" diagrams in the RE
  • Reference genomes within the Research Environment
  • Using VEP with the LOFTEE plugin
  • If I think I have found a variant that I believe is pathogenic, who should I tell?

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Last update: November 27, 2023