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Extracting variants for multiple read groups with VariantsToTable

s_andrewss_andrews Cambridge, UKMember

I have a VCF file representing several related individuals and I want to extract the information into a table using VariantsToTable. All I really need is the genotype for each individual in the set at each variant position. I've tried extracting with VariantsToTable but can't find a way to separate the different read groups in the output, or to get a simple text representation of the genotype at each position.

I can see all of the information I need when I load the file into IGV so I'm guessing there must be a simply way to do this that I'm missing?

Any help is much appreciated.


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