idx=/nfs/srv/databases/ngs/russal2010/index/chr19.idx
trim='java -jar /nfs/srv/databases/ngs/suvorova/trimmomatic/trimmomatic-0.30.jar'
reads=/nfs/srv/databases/ngs/russal2010/reads/chr19.fastq
trim_reads=/nfs/srv/databases/ngs/russal2010/reads/chr19_trimmed.fastq
wdir=/nfs/srv/databases/ngs/russal2010
samfile=${wdir}/map/chr19_aln.sam
bamfile=${wdir}/map/chr19_aln.bam
sortedbam=${wdir}/map/chr19_alnsrt.bam
flag_out=${wdir}/map/flgst.txt
ref=${wdir}/chr19.fasta
refg=${wdir}/refgene.txt
dbsnp=${wdir}/dbsnp.txt
genomes=${wdir}/1000g.txt
gwas=${wdir}/gwas.txt
clinvar=${wdir}/clinvar.txt
avdir=/nfs/srv/databases/annovar