Hi GATK team,
I ran the haplotypcaller on a single mapped bam file. Command:
java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I MyMappedSample.bam --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -o MyMappedSample.g.vcf -L hg38.exome.regions.bed
From this output, I am running the GenotypeGVCFs. Command:
java -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R Homo_sapiens_assembly38.fasta --variant MyMappedSample.g.vcf -o MyMappedSample.geontyped.vcf -nt 32 -L hg38.exome.regions.bed
The issue that I am is that when running the GenotypeGVCFs, even though I have the "-nt" flag, it is not using multiple threads, and only running with a single thread. I am only running this on a single sample. I am using version 3.5 (we have not yet updated our system to a java 8). Is this an issue with version 3.5, and I should maybe try an earlier version?
