Whats is the best way to identify shared rare variants in cousin families. I have done the exome sequencing and called the SNPs using GATK.
Can you clarify some details of your experiment? What subjects have data available? What are you looking for? Just shared variants? Or variants in a single gene causative of a rare disorder? Do you have data from the parents? I assume by "cousin families" you mean there is some consanguineous relationship in the pedigree -- but at what level in the pedigree? Do you have data from those individuals? These details will help give you a reasonable answer to your question, since there a lot of ways you could go about this. What have you tried?
I am sorry for not being explanatory in the question. I am looking for identification of disease causing rare variants. I dont have the SNP data from parents. I have sequenced the affected siblings and cousins and there is no consanguineous relationship. I have identified the variants present in each of the sibling and cousin individual separately. Now I am trying to look for variants shared by all the three affected members (predicting that might be the causative variants). I hope this explanation will help in understanding the question.
I suggest you try transmission disequibrium test (TDT) or family based association test. Your ability to identify the causal variants will of course depend on your sample size and characteristics, and also on the number of prior candidate SNPs you have.
Thanks Fabio Marroni.
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