Set RAM provided to JVM

[jasonwalker80]

Do we need to set the amount of RAM we are providing to the JVM?

docker-cle/mapq0_vcf_filter.sh

Line 48 in 1408188

java -jar /opt/GenomeAnalysisTK.jar -T VariantFiltration -R $ref_fasta -o $outdir/mapq_filtered.vcf.gz --variant $outdir/mapq0.vcf --filterExpression "((MQ0*1.0) / (DP*1.0)) > $mapq0perc" --filterName "MAPQ0"