/usr/local/bin/samtools mpileup -B -f ${h37}sami.fasta ${dir}processed/${bamfile} > ${dir}processed/${bamfile}.mpileup 
/usr/bin/java -Xmx16g -jar /usr/local/share/GenomeAnalysisTK.jar -T UnifiedGenotyper -R ${h37}sami.fasta -I ${dir}processed/${bamfile} -o ${dir}processed/${bamfile}.flt.vcf -glm BOTH -mbq 13 -nct 6 -nt 4 -A BaseCounts -A VariantType -rf BadCigar > /dev/null