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Are you going to have a working version in few time of the complete GATK Best Practices in Spark?
I am trying to use your Spark commands in GATK 4 release in order to execute the GATK Best Practices with Spark and it looks working fine until the BQSRPipelineSpark (I am using gatk_4/build/libs/gatk-package-4.beta.5-67-ge919f85-SNAPSHOT-local.jar with openjdk version "1.8.0_131" on a single node with 27.5 GB RAM and 4 execution threads); but when I try to execute HaplotypeCallerSpark I noticed that there are some unresolved issues (reported on other questions in GATK forums too).
For example, as personal experience I tried to execute
./gatk-launch ReadsPipelineSpark --input ERR000589_aligned.bam --reference ucsc.hg19.2bit --disableSequenceDictionaryValidation true --knownSites dbsnp_138.hg19.vcf --knownSites Mills_and_1000G_gold_standard.indels.hg19.vcf --knownSites 1000G_phase1.indels.hg19.sites.vcf --emitRefConfidence GVCF --output ERR000589_raw_variants.g.vcf
that according to the output of gatk-launch --list
ReadsPipelineSpark (BETA Tool) Takes aligned reads (likely from BWA) and runs MarkDuplicates, BQSR, and HaplotypeCaller. The final result is analysis-ready variants
contains HaplotypeCaller; in particular, I guess that the execution never ends (or it takes too much time) because I executed the program all night long, without reaching the end of the execution of this command; I attached part of the command output and I even tried to google some WARN line, but I was not able to interpret them.
There was the same behavior even when I tried to execute HaplotypeCallerSpark.
So is the problem mine, in the execution of the command? Or it is a problem of HaplotypeCallerSpark which is not again mature? And in case this second option is true, I am interested to know if GATK staff is working on it and if we will have a working version in few time or we will have to wait for much time?
Because in case I could consider to look at other "Sparkified" solutions for the GATK Best Practices following steps (Haplotype Caller, Genotype GVCF, Variant Annotation...).
Thanks for your time,