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2 hours ago by

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 HaplotypeCaller --> 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 .ped file(tried))

Does anybody have a clue how to work this around?

Thank you very much in advance for any help!


modified 2 hours ago

2 hours ago


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