39 lines
1.3 KiB
Bash
39 lines
1.3 KiB
Bash
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thread=1
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#n_r1=~/data/fastq/ZY2105177532213000/n_r1.fq
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#n_r2=~/data/fastq/ZY2105177532213000/n_r2.fq
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#n_r1=~/data/fastq/ZY2105177532213000/sn_r1.fq
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#n_r2=~/data/fastq/ZY2105177532213000/sn_r2.fq
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#reference=~/data/reference/human_g1k_v37_decoy.fasta
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#n_r1=~/fastq/sn_r1.fq
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#n_r2=~/fastq/sn_r2.fq
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#n_r1=~/fastq/ssn_r1.fq
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#n_r2=~/fastq/ssn_r2.fq
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#n_r1=~/fastq/tiny_n_r1.fq
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#n_r2=~/fastq/tiny_n_r2.fq
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n_r1=~/fastq/diff_r1.fq
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n_r2=~/fastq/diff_r2.fq
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#n_r1=~/fastq/d_r1.fq
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#n_r2=~/fastq/d_r2.fq
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reference=~/reference/human_g1k_v37_decoy.fasta
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#out=./ssn.sam
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out=./out.sam
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#out=/dev/null
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#time ./bwa mem -t 12 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
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# /home/zzh/data/reference/human_g1k_v37_decoy.fasta \
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# /home/zzh/data/fastq/nm1.fq \
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# /home/zzh/data/fastq/nm2.fq -o /dev/null
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#time ./bwa mem -t 12 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
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# /home/zzh/data/reference/human_g1k_v37_decoy.fasta \
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# /mnt/d/data/fastq/ZY2105177532213000/ZY2105177532213010_L4_1.fq.gz \
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# /mnt/d/data/fastq/ZY2105177532213000/ZY2105177532213010_L4_2.fq.gz \
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# -o /dev/null
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time ./bwa mem -t $thread -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
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$reference \
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$n_r1 \
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$n_r2 \
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-o $out
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