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GenotypeGVCFs on more than 300 WGS human samples
Recently I got some problem during running GenotypeGVCFs on my 360 WGS samples.
My samples are human 15X whole-genome sequencing data.
I made 360 gvcf files by running HaplotypeCaller for each sample.
But when I run GenotypeGVCFs with the default parameters, it showed the estimated time as 1000 weeks.
I tried to combine gvcfs by using CombineGVCFs and tried to run GenotypeGVCFs on these combined vcfs, it failed due to the memory shortage, I allocated 400G for java heap though.
Is there any guideline for running GenotypeGVCFs efficiently to many samples?