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everestial / VCF-Simplify

A python parser to simplify and build the VCF (Variant Call Format).
MIT License
47 stars 11 forks source link

Is if possible for VCF-Simplify to convert non-dosage vcf to dosage vcf? #8

Open ConnieXuhm opened 3 years ago

ConnieXuhm commented 3 years ago

Dear developer, I am trying to acquire the dosage VCF file converted from .gen format. However, qctools and other conversion can only output the non-dosage VCF, which cannot meet my demand of the following investigation. Then I find out that maybe Pysam can do this, but I am not quite familiar with the complex code. I want to know if this VCF-Simplify can achieve this function? Many thanks! Hope for your reply!

everestial commented 3 years ago

Hi @ConnieXuhm

Please share your VCF file (both dosage and non-dosage) so I can tell if it can do what you want it to do.

For a more controlled and custom VCF parsing you may use https://github.com/everestial/vcfparser but this application is still waiting for few more changes and updates.

Let me know if you have any other questions.