thread=64

## d1 k18<=4 89%
#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_wes_144/1w_1.fq
#n_r2=~/data/fastq/dataset/na12878_wes_144/1w_2.fq
#n_r1=~/data/fastq/dataset/na12878_wes_144/ss_1.fq
#n_r2=~/data/fastq/dataset/na12878_wes_144/ss_2.fq
#n_r1=~/data/fastq/dataset/na12878_wes_144/45m_r1.fq
#n_r2=~/data/fastq/dataset/na12878_wes_144/45m_r2.fq
#n_r1=~/data/fastq/dataset/na12878_wes_144/45mr1.fq.gz
#n_r2=~/data/fastq/dataset/na12878_wes_144/45mr2.fq.gz
## d2 <= 4 87%
#n_r1=~/data/fastq/dataset/na12878_wgs_101/na12878_r1.fq
#n_r2=~/data/fastq/dataset/na12878_wgs_101/na12878_r2.fq
#n_r1=~/data/fastq/dataset/na12878_wgs_101/s_1.fq
#n_r2=~/data/fastq/dataset/na12878_wgs_101/s_2.fq
#n_r1=~/data/fastq/dataset/na12878_wgs_101/45m_r1.fq
#n_r2=~/data/fastq/dataset/na12878_wgs_101/45m_r2.fq
# d3 <= 4 77%
#n_r1=~/data/fastq/dataset/na12878_wgs_150/s_1.fq
#n_r2=~/data/fastq/dataset/na12878_wgs_150/s_2.fq
#n_r1=~/data/fastq/dataset/na12878_wgs_150/45mr1.fq.gz
#n_r2=~/data/fastq/dataset/na12878_wgs_150/45mr2.fq.gz
## d4 <= 4 93%
#n_r1=~/data/fastq/dataset/zy_wes/s_1.fq
#n_r2=~/data/fastq/dataset/zy_wes/s_2.fq
#n_r1=~/data/fastq/dataset/zy_wes/45mr1.fq.gz
#n_r2=~/data/fastq/dataset/zy_wes/45mr2.fq.gz
## d5 <= 4 80%
#n_r1=~/data/fastq/dataset/zy_wgs/45mr1.fq.gz
#n_r2=~/data/fastq/dataset/zy_wgs/45mr2.fq.gz
#n_r1=~/data/fastq/dataset/zy_wgs/s_1.fq
#n_r2=~/data/fastq/dataset/zy_wgs/s_2.fq
n_r1=~/data1/fastq/dataset/zy_wgs/E150010395_L01_690_1.fq
n_r2=~/data1/fastq/dataset/zy_wgs/E150010395_L01_690_2.fq

reference=~/data1/fmt_ref/human_g1k_v37_decoy.fasta
#reference=~/reference/bwa/human_g1k_v37_decoy.fasta
#reference=~/data/reference/human_g1k_v37_decoy.fasta

#out=~/data1/out-u8-1.sam
#out=~/data1/out-i16.sam
#out=~/data1/fmt-out.sam
out=~/data/fastbwa.ert.sam
#out=/dev/null

time ./fastbwa mem -t $thread -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
    $reference \
    $n_r1 \
    $n_r2 \
    -o $out -2 -Z