4 ms·

can't get it to use any data sets that i have in the normal .vcf formats, etc

by cryoshon 8y ago

Beefin 8y ago
What testing providers share your raw genome in an .vcf format?
- searine 8y ago
  Nobody shares your genome. Promethease though allows for gvcfs and other formats so that you can upload more comprehensive sequencing data with full coverage.
  - Beefin 8y ago
    Maybe I should've rephrased... my question is which genetic testing providers give you a raw genome file in .vcf format? If none then I think we're talking about two different things. https://customercare.23andme.com/hc/en-us/articles/212196868-Accessing-and-Downloading-Your-Raw-Data https://customercare.23andme.com/hc/en-us/articles/212196868...
    - searine 8y ago
      23andme is casual genetics, and misses a lot of the variants that are important clinically. These ancestry sites are the entry point, but not the definitive answer. SNP chips are on the way out and whole genome/whole exome are becoming much cheaper. For many people (myself included) who are trying to diagnose a disease or understand our personal genetics at a base-pair resolution then VCF is the standard format. Ancestry and 23andme use proprietary formats but all independent labs/clinics/commercial operations use VCF and it is the format that patients will have. If a patient is dropping a grand or three to get their personal genome, they are going to be receiving the raw data in VCF or BAM. As a side note, your site asks if people "had their genome sequenced" but 23andMe results aren't a genome. It is a peek at a fraction of the genome. Your site doesn't accept whole genome data. Also, if by "offices" you mean doctors offices or any kind of medical professional, then you are putting them at risk. Variant calls delivered to patients from a medical professional need oversight. Calls need to be made in a CLIA laboratory and pass through a genetic counselor. It is fine to skirt regulations if an individual is analyzing their own genome, but once you insert a third party, then you are bring in legal issues, reporting issues, and HIPAA issues.
      - calvano915 8y ago
        Your comment was very insightful. I've considered 23andme and similar services before, and it is helpful to understand that a fractional amount of one's genome is all that is provided/analyzed. I'm excited to see that whole sequencing has broken the $1000 barrier some time ago, and was available recently for $200 as a promotion! (https://www.wired.com/story/whole-genome-sequencing-cost-200-dollars/ https://www.wired.com/story/whole-genome-sequencing-cost-200...)

can't get it to use any data sets that i have in the normal .vcf formats, etc

Beefin 8y ago

What testing providers share your raw genome in an .vcf format?

searine 8y ago
Nobody shares your genome. Promethease though allows for gvcfs and other formats so that you can upload more comprehensive sequencing data with full coverage.
- Beefin 8y ago
  Maybe I should've rephrased... my question is which genetic testing providers give you a raw genome file in .vcf format? If none then I think we're talking about two different things. https://customercare.23andme.com/hc/en-us/articles/212196868-Accessing-and-Downloading-Your-Raw-Data https://customercare.23andme.com/hc/en-us/articles/212196868...
  - searine 8y ago
    23andme is casual genetics, and misses a lot of the variants that are important clinically. These ancestry sites are the entry point, but not the definitive answer. SNP chips are on the way out and whole genome/whole exome are becoming much cheaper. For many people (myself included) who are trying to diagnose a disease or understand our personal genetics at a base-pair resolution then VCF is the standard format. Ancestry and 23andme use proprietary formats but all independent labs/clinics/commercial operations use VCF and it is the format that patients will have. If a patient is dropping a grand or three to get their personal genome, they are going to be receiving the raw data in VCF or BAM. As a side note, your site asks if people "had their genome sequenced" but 23andMe results aren't a genome. It is a peek at a fraction of the genome. Your site doesn't accept whole genome data. Also, if by "offices" you mean doctors offices or any kind of medical professional, then you are putting them at risk. Variant calls delivered to patients from a medical professional need oversight. Calls need to be made in a CLIA laboratory and pass through a genetic counselor. It is fine to skirt regulations if an individual is analyzing their own genome, but once you insert a third party, then you are bring in legal issues, reporting issues, and HIPAA issues.
    - calvano915 8y ago
      Your comment was very insightful. I've considered 23andme and similar services before, and it is helpful to understand that a fractional amount of one's genome is all that is provided/analyzed. I'm excited to see that whole sequencing has broken the $1000 barrier some time ago, and was available recently for $200 as a promotion! (https://www.wired.com/story/whole-genome-sequencing-cost-200-dollars/ https://www.wired.com/story/whole-genome-sequencing-cost-200...)