thread=32
n_r1=~/fastq/na12878/na12878_r1.fq
n_r2=~/fastq/na12878/na12878_r2.fq
reference=~/reference/human_g1k_v37_decoy.fasta
out=/dev/null
time /home/zzh/work/sbwa/bwa mem -t $thread -b 256 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
    $reference \
    $n_r1 \
    $n_r2 \
    -o $out