Hi,
I am currently working on making a variants database.
I generate seperate VCF files for each samples them and merge them using VCFtools (using mergeVCF command) to make a multisample VCF file. Then I can calculate the Minor Allele Frequency using VCFtools for each variant in the multisample VCF file.
My question is, what is your recommendation about the best way to proceed. Do you recommend any other pipeline? Please also correct me if I am wrong in choosing the pipelines mentioned above.
Thank you.
@Shifu Chen
But you think that will not be very complex to update the new records (new samples). we need to add new rows and new columns every time and the number of variant increase very fast so there is no limitation of the size ??
The issue is non-trivial:
https://academic.oup.com/database/article/doi/10.1093/database/bax049/3953981
but you can try to start with whatever database that works for you. Still, some type of queries may be not possible to run du to the performance.
I have always used an excel file with anonymised patient numbers vertically and the polymorphisms horizontally with patient details, such as demographics, blood results, symptom details, pathogenesis etc included, then the data can be edited and transferred to statistical programmes like SPS or whatever is current. Probably very old fashioned, I know. Sorry, I can't comment on VCF files but find excel much the same as writing in a log book to contain all information until it needs to be analysed. It can also be copied and pasted easily and a many times as required while always keeping a master original of the data. Good look!
@Michal Okoniewski
Thank you for the publication it will be very halpful
cheers,
@Annwyne Houldsworth
Thank you but With Excel it will be very hard to work due to the limitation of the size since the Data is very big and constantly increasing. I already used this method in the beginning associated with the program R.
Best,
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