Experience with BaseRecalibratorSpark and ApplyBQSRSpark

Question

[nhaus]

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!

Answer 1

[colindaven]

I haven't used that tool, but you might want to consider elprep too if you have RAM to burn:

elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files