Open leorippel opened 3 years ago
The disk is basically used for external sorting the input gvcf data, so it'll need roughly their same size. I'd be surprised if it used less than half or more than double, depending on what gzip compression level was used to create the inputs.
The external sorting is an alternative to having to fit all of the inputs in memory or try to keep 100K's of files open at once, of course.
I am using glnexus_cli to jointly genotype ~2,000 WGS gVCFs generated by GATK. Total gVCF size is less than 15TB but GLnexus.DB directory is currently at 47TB and still running. Is this behavior normal? I've included chr1-22, X, Y in a single BED file.
A related question. Is there any way to estimate the approximate time to completion while running from the LOG messages?
Hi,
The GLnexus team have an estimation of how much space in HD is required, compared to the sizes of the .gvcfs?
Cheers.