thread=1
n_r1=~/data/fastq/dataset/na12878_wgs_150/diff_r1.fq
n_r2=~/data/fastq/dataset/na12878_wgs_150/diff_r2.fq
#n_r1=~/data/fastq/dataset/na12878_wes_144/diff_r1.fq
#n_r2=~/data/fastq/dataset/na12878_wes_144/diff_r2.fq
#n_r1=~/data/fastq/ZY2105177532213000/n_r1.fq
#n_r2=~/data/fastq/ZY2105177532213000/n_r2.fq
#n_r1=~/data/fastq/ZY2105177532213000/sn_r1.fq
#n_r2=~/data/fastq/ZY2105177532213000/sn_r2.fq
#reference=~/data/reference/human_g1k_v37_decoy.fasta
#n_r1=~/fastq/sn_r1.fq
#n_r2=~/fastq/sn_r2.fq
#n_r1=~/fastq/ssn_r1.fq
#n_r2=~/fastq/ssn_r2.fq
#n_r1=~/fastq/tiny_n_r1.fq
#n_r2=~/fastq/tiny_n_r2.fq
#n_r1=~/fastq/diff_r1.fq
#n_r2=~/fastq/diff_r2.fq
#n_r1=~/fastq/diff_all_r1.fq
#n_r2=~/fastq/diff_all_r2.fq
#n_r1=~/fastq/d_r1.fq
#n_r2=~/fastq/d_r2.fq
reference=~/reference/human_g1k_v37_decoy.fasta
#out=./ssn.sam
out=./out.sam
#out=/dev/null
#time ./bwa mem -t 12 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
#    /home/zzh/data/reference/human_g1k_v37_decoy.fasta \
#    /home/zzh/data/fastq/nm1.fq \
#    /home/zzh/data/fastq/nm2.fq -o /dev/null

#time ./bwa mem -t 12 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
#    /home/zzh/data/reference/human_g1k_v37_decoy.fasta \
#    /mnt/d/data/fastq/ZY2105177532213000/ZY2105177532213010_L4_1.fq.gz \
#    /mnt/d/data/fastq/ZY2105177532213000/ZY2105177532213010_L4_2.fq.gz \
#    -o /dev/null

time ./bwa mem -t $thread -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
    $reference \
    $n_r1 \
    $n_r2 \
    -o $out