Why GATK is slow with haplotypecalling

Question

[rj.rezwan]

Hi, I am using GATK for haplotypecalling analysis. My reference genome size is 1.33 GB. It takes an average of 6 days to complete the analysis of each genotype. The size of the genotype.bam file is 26 GB. Why it takes too much time?

[Pierre Lindenbaum]

spit your reference into parts (eg. using https://gatk.broadinstitute.org/hc/en-us/articles/360041416072-ScatterIntervalsByNs-Picard- ) and call each interval in parallel .