thread=1
#n_r1=~/data/fastq/dataset/na12878_wgs_150/bn1.fq
#n_r2=~/data/fastq/dataset/na12878_wgs_150/bn2.fq
#n_r1=~/data/fastq/dataset/na12878_wes_144/SRR25735653_1.fastq
#n_r2=~/data/fastq/dataset/na12878_wes_144/SRR25735653_2.fastq
#n_r1=~/data/fastq/dataset/na12878_wgs_150/n1.fq
#n_r2=~/data/fastq/dataset/na12878_wgs_150/n2.fq
#n_r1=~/data/fastq/dataset/na12878_wgs_101/na_1.fq
#n_r2=~/data/fastq/dataset/na12878_wgs_101/na_2.fq
n_r1=~/data/fastq/dataset/zy_wes/sn1.fq
n_r2=~/data/fastq/dataset/zy_wes/sn2.fq


#n_r1=~/data/fastq/zy/wgs/n1.fq
#n_r2=~/data/fastq/zy/wgs/n2.fq
#n_r1=~/data/fastq/ds/n1.fq
#n_r2=~/data/fastq/ds/n2.fq
#n_r1=~/data/fastq/platinum/n1.fq
#n_r2=~/data/fastq/platinum/n2.fq
#n_r1=~/data/fastq/zy/t1.fq
#n_r2=~/data/fastq/zy/t2.fq
#n_r1=~/data/fastq/zy/n1.fq
#n_r2=~/data/fastq/zy/n2.fq
#n_r1=~/data/fastq/ds/d1_1.fq
#n_r2=~/data/fastq/ds/d1_2.fq
#n_r1=~/data/fastq/ds/d2_1.fq
#n_r2=~/data/fastq/ds/d2_2.fq
#n_r1=~/data/fastq/ds/wes/n1.fq
#n_r2=~/data/fastq/ds/wes/n2.fq
#n_r1=~/fastq/ZY2105177532213010_L4_1.fq
#n_r2=~/fastq/ZY2105177532213010_L4_2.fq
#n_r1=~/data/fastq/na12878/nas_1.fq
#n_r2=~/data/fastq/na12878/nas_2.fq
#n_r1=~/data/fastq/na12878/na_1.fq
#n_r2=~/data/fastq/na12878/na_2.fq
#n_r1=~/fastq/na12878/na12878_r1.fq
#n_r2=~/fastq/na12878/na12878_r2.fq
#n_r1=~/fastq/n_r1.fq
#n_r2=~/fastq/n_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=~/data/fastq/sn_r1.fq
#n_r2=~/data/fastq/sn_r2.fq
#n_r1=~/data/fastq/ssn_r1.fq
#n_r2=~/data/fastq/ssn_r2.fq
#n_r1=~/fastq/ERR194147_1_120w.fastq
#n_r2=~/fastq/ERR194147_2_120w.fastq
#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/d_r1.fq
#n_r2=~/fastq/d_r2.fq
reference=~/data/reference/human_g1k_v37_decoy.fasta
#out=./all.sam
#out=./sn.sam
#out=./ssn-x1.sam
out=./out.sam
#out=/dev/null
#out=./na12878.sam
#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 -b 256 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
    $reference \
    $n_r1 \
    $n_r2 \
    -o $out -2