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:
gs://gatk-test-data/intervals/hg38.even.handcurated.20k.intervals

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.

Answers

Sign In or Register to comment.