GATK4 JointGenotype workflow unpadded intervals for hg19
Dear GATK Team,
I'm trying to run the JointGenotype workflow (https://github.com/gatk-workflows/broad-prod-wgs-germline-snps-indels/JointGenotypeWf.wdl) on hg19 whole genome data.
(I'm using Google Cloud Platform)
I was able to run hg38 workflow with test data.
But the trouble I'm having now is to have unpadded intervals file as used in hg38 workflow:
I'm thinking to liftover these intervals to hg19. How do you think this will affect the genotype result?
If I have to prepare the intervals myself,
is there any documentation how the hg38 intervals were generated, as a reference?
Thank you in advance.