srun java -XX:ParallelGCThreads=2 -Xmx12g -jar GenomeAnalysisTK.jar -T VariantFiltration -V scaf_2_chr_BI_BP.vcf -R alygenomes.fasta --genotypeFilterExpression "DP > 4" --genotypeFilterName "DPPASS" -o scaf_2_chr_BI_BP_COVFAIL.list -L scaffold_2:248000-248103 printf "\nFinished\n\n"