2016/11/06 14:57:44: DEBUG Enqueuing command:
#TASK tags=Sample_5
gatk -T VariantFiltration \
-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_haplotype.realigned.withrg.csorted.cleaned.aligned.vcf \
–filterExpression “QD ‘<’ 2.0 || FS ‘>’ 60.0 || MQ ‘<’ 40.0 || MQRankSum ‘<’ -12.5 || ReadPosRankSum ‘<’ -8.0” \
–filterName “my_snp_filter” \
-o /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_my_snp_filter.haplotype.realigned.mdup.csorted.cleaned.aligned.vcf
2016/11/06 14:57:48: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 04 seconds