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PharmGKB / PharmCAT

The Pharmacogenomic Clinical Annotation Tool
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OA and CNV Data from QuantStudio 12K Flex #172

Open Estefany2081 opened 7 months ago

Estefany2081 commented 7 months ago

Hello I work for a lab that performs PGX We use QuantStdio 12K Flex in order to run CNV and OA Both of these give us CSV and .TXT files In order to use PahrmCat, the requirement is a VCF file However, I cannot download my OA or CNV as a VCF How can I best convert my CSV file into VCF file in order to use on PharmaCat?

Thank you very much

markwoon commented 7 months ago

One of the requirements of PharmCAT is that it requires VCF.

We cannot advise you on how to get VCF for your data as there are too many considerations that needs to be taken into account.

whaleyr commented 7 months ago

@Estefany2081 To be a bit more specific: CSV and TXT files are unstructured and could contain any type of data. VCF is a community standard and a very specific format that has strict rules for how data is structured.

There's no way for us to write a "CSV/TXT to VCF converter" with no knowledge of what's in the original data. Writing data conversion code for one specific device is outside the scope of this project. Since you're using data from a very specific device from a very specific manufacturer either you need to write the converter yourself or ask ThermoFisher to add support for VCF export.

BinglanLi commented 6 months ago

@Estefany2081 We would love to follow up with you on the issue. While we cannot guarantee a feature for CSV soon, it is still of interest to us. Can you share a mock example of your CSV file? It will be really helpful.

Estefany2081 commented 6 months ago

Yes I’ll send it over when I get to the lab Thank you guys so much Thankfully translational was able to finish for us but I would love to be able to provide the csv file and see if it helps you guys as well

On Wed, Mar 6, 2024 at 6:13 PM Binglan Li @.***> wrote:

@Estefany2081 https://github.com/Estefany2081 We would love to follow up with you on the issue. While we cannot guarantee a feature for CSV soon, it is still of interest to us. Can you share a mock example of your CSV file? It will be really helpful.

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markwoon commented 3 weeks ago

@Estefany2081 Just following up - do you have an example CSV file available?