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Should intervals overlap for the GenotypeGVCF step when calling genotypes on RNAseq data?

NiekdeKleinNiekdeKlein GroningenMember

I have gVCFs from RNAseq data and want to run GenotypeGVCF on multiple intervals per chromosome. Although the reads are mostly only from exons I still want to run GenotypeGVCF on the complete chromosome. For exome sequencing it is suggested to add -ip for the padding around genes, but since I want to include the whole chromosome I'm not sure if I should overlap the intervals or make them adjacent, and if I should add padding or not.

e.g. should it be

chr1:100-200
chr1:201-300

or

chr1:100-200
chr1:150-250

and should -ip be set to 0 or not?

Thanks for your help!
Niek

Answers

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