Hello everybody,
I am currently setting up a variant calling pipeline for WGS using GATK4. As part of this, Base quality score recalibration is essential. Since GATK4 there is the option to parallelize this with spark
. Using this option leads to the Warning
Warning: ApplyBQSRSpark is a BETA tool and is not yet ready for use in production
On their homepage it is also specified that ApplyBQSRSpark
is a BETA version.
During my tests however, I did not notice a difference between the "stable" single core ApplyBQSR
with regard to the results. However, I didn't tried many BAM files yet. Because the speed up with ApplyBQSRSpark
is enormous, I would really like to use that.
I was wondering if someone of you has experience with ApplyBQSRSpark
and whether it outputs the same variants in the end.
Cheers!