45 lines
1.5 KiB
Bash
Executable File
45 lines
1.5 KiB
Bash
Executable File
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=~/data1/fmt_ref/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 ./fastbwa mem -t $thread -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
|
|
$reference \
|
|
$n_r1 \
|
|
$n_r2 \
|
|
-o $out
|
|
|
|
|