GATK18.104.22.168 beta version
b) Exact command used:
java -jar gatk-package-22.214.171.124-local.jar DepthOfCoverage -R genome.fa -I recal.bam -O recal.depcov -L Homosapiens_hg19.bed --summary-coverage-threashold 15 --omit-depth-output-at-each-base true --omit-interval-statistics true
If not an error, choose a category for your question(REQUIRED):
a) How do I decrease the analysis spending time?
Previous GATK3 version had a '-nt' threads option to increase the analysis velocity.
I tried to cut down on the work time but couldn't find any option related with reducing operation time.
Some person posted about the same issue: https://gatk.broadinstitute.org/hc/en-us/community/posts/360071895391-Speeding-up-GATK4-DepthOfCoverage
I think GATK4 takes a long time to analysis compare with GATK3 version (it spent only 30 min for analysis)
Could you give some advice for solving this issue?
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