Allow VCF format for input of genotype data

[amanicha]

It would be very helpful if ProbABEL could take VCF as input. VCF has become one of the most useful formats for genotype data, particularly as the Michigan imputation server is providing results this way. Imputation results are getting larger due to expanded reference panels, so that the MLDOSE format with one individual per row can be cumbersome as it requires all data to be read in before proceeding with regression analyses.

[lckarssen]

Thanks for reporting this! I agree that the ability to use VCF as input format would be a valuable addition for ProbABEL.

I guess the VCFlib C++ library would be a good place to start. Alternatively, htslib (in C) could be an option. From a quick look it seems that licence-wise both could be included in/distributed with ProbABEL.

Unfortunately I don't have much time to work on this, so any help is appreciated!