45 lines
1.4 KiB
Bash
Executable File
45 lines
1.4 KiB
Bash
Executable File
thread=1
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## d1
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n_r1=~/data/fastq/dataset/na12878_wes_144/s_1.fq
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n_r2=~/data/fastq/dataset/na12878_wes_144/s_2.fq
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## d2
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#n_r1=~/data/fastq/dataset/na12878_wgs_101/s_1.fq
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#n_r2=~/data/fastq/dataset/na12878_wgs_101/s_2.fq
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# d3
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#n_r1=~/data/fastq/dataset/na12878_wgs_150/s_1.fq
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#n_r2=~/data/fastq/dataset/na12878_wgs_150/s_2.fq
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## d4
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#n_r1=~/data/fastq/dataset/zy_wes/s_1.fq
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#n_r2=~/data/fastq/dataset/zy_wes/s_2.fq
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## d5
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#n_r1=~/data/fastq/dataset/zy_wgs/s_1.fq
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#n_r2=~/data/fastq/dataset/zy_wgs/s_2.fq
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#reference=~/reference/bwa/human_g1k_v37_decoy.fasta
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reference=~/data/reference/human_g1k_v37_decoy.fasta
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#out=./all.sam
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#out=./sn.sam
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#out=./ssn-x1.sam
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#out=./out.sam
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out=/dev/null
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#out=./na12878.sam
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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 ./fastbwa mem -t $thread -b 256 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
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$reference \
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$n_r1 \
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$n_r2 \
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-o $out -2
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