Entering edit mode
9 weeks ago
rj.rezwan • 0
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?
spit your reference into parts (eg. using https://gatk.broadinstitute.org/hc/en-us/articles/360041416072-ScatterIntervalsByNs-Picard- ) and call each interval in parallel .