haplotype phasing with SHAPIT

Question

[jahn.davik]

Hello everyone, I am totally new to the phasing area and have a (trivial) question: I want to phase my organism. I have a reference genome and I have SNP data provided by a commercial vendor. The SNP data comes in the standard format with positional data etc., and the SNP data in AB-format. My question: are these data useful for phasing with Shapeit?

Thanks, jahn

[4galaxy77]

What's your organism? Can you also edit into your question post a couple of lines of your data (make sure to wrap them in them in code tags). Unfortunately in genetics there is no 'standard format' :)