Hello
When I got the results of WES in vcf format, it showed that two patients, who are supposed to be sibling, are not. I used plink for IBS/IBD estimation but didn't know how to do it (first time using plink or any other tool ). Could you please help me find a way to double-check the results. Thank you
Not plink but time ago we published relationship computing from NGS data here:
pardon my ignorance, but in my opinion you're conclusion might be wrong in case it's based on the two individuals only, unless you compare to their respective parents, too. Two siblings can share anything between 100% and 0% of the same genetic material. The only given is 50% shared DNA to each parent.
Or am I wrong there?
Any evidence one may get from using IBS/IBD scores would be inconclusive at best owing to the range of variation, as you rightly point out. Identical twins are siblings as well, and will share the Z0, Z1, Z2 values with duplicated samples. It is not possible to conclusively decide that two samples are siblings from SNV data without access to the parental SNVs as well.
You fail to mention a couple of crucial details, for example:
Please provide these information otherwise it's difficult to help you effectively.