2016/11/06 11:53:54: DEBUG Enqueuing command:
#TASK tags=Sample_5
gatk -T HaplotypeCaller \
-R /scratch/Reference_Genomes/Public/Vertebrate_mammalian/Homo_sapiens/ENSEMBL-release-81-GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa \
-I /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_realigned.withrg.csorted.cleaned.aligned.bam \
-stand_emit_conf 10 -stand_call_conf 30 –genotyping_mode DISCOVERY \
-o /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_haplotype.realigned.withrg.csorted.cleaned.aligned.vcf
2016/11/06 14:57:32: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 183 minutes, 38 seconds