Hello,
I have a cohort of several sibling pairs, and I am interested in finding Germline SNPs for each pair. Furthermore, I understand from the best practices that a joint analysis using the Haplotype Caller works very well. I am not sure how to proceed. Is it reasonable/possible to do the following?:
1) Haplotype Caller to find SNPs between each pair <- is this possible with the Haplotype caller? It seems like it is meant to handle one or more samples against a single reference sequence.
2) Joint genotyping using then haplotype caller
Thank you in advance, any help appreciated,
Ramiro
