Use of GATK HaplotypeCallerSpark
0
0
Entering edit mode
17 months ago

Hi all,

I wanted to post this question to the GATK support forum, but I can't for the life of me figure out how to do it, so here it goes.

How bad exactly is it to use HaplotypeCallerSpark in GATK 4.0.2.1? I realize it's in beta, but I'm wondering if that means "your results will be useless" or just "use with caution". The reason I'm asking that is because it seems like Spark is the only way to multi-thread in GATK 4.

Here's an example of my usage:

gatk --java-options  "-Xmx32g -XX:ParallelGCThreads=1" HaplotypeCallerSpark --spark-master local[20] -R myref.1.2bit -I mybam.bam -O tmygvcf.g.vcf --emit-ref-confidence GVCF --min-dangling-branch-length 1 --min-pruning 1
GATK • 545 views
ADD COMMENT

Login before adding your answer.

Traffic: 2056 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6