Hi, I got some monozygotic twins samples (and a technical replicate of the same sample sequences twice) and I am running a
GATK GenotypeGVCFs on their
GATK HplotypeCaller called variants (through single
GenomicsDBImport data aggregation -->
GenotypeGVCFs as per GATK joint calling guidelines). This last step adds a ExcessHet annotation that is later used in VQSR filtering but it specifies that:
If samples are known to be related, a pedigree file can be provided so that the calculation is only performed on founders and offspring are excluded.
I got no relative samples and only monozygotic twins offsprings couples, how do I specify that in a
.ped file? (I cannot specify that they are the same sample as they have different names in
GenomicsDBImport and if I just specify the same family ID it makes absolutely no difference with the version in which I do not provide
Does anybody have a clue how to work this around?
Thank you very much in advance for any help!