25 lines
580 B
Bash
Executable File
25 lines
580 B
Bash
Executable File
thread=1
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n_r1=~/data/dataset/real/D1/n1.fq.gz
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n_r2=~/data/dataset/real/D1/n2.fq.gz
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#n_r1=~/data/dataset/real/D3/n1.fq.gz
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#n_r2=~/data/dataset/real/D3/n2.fq.gz
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#n_r1=~/data/dataset/real/D3/n1.fq
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#n_r2=~/data/dataset/real/D3/n2.fq
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#n_r1=~/data/t120w-1.fq
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#n_r2=~/data/t120w-2.fq
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#n_r1=~/data/1w-1.fq
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#n_r2=~/data/1w-2.fq
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reference=~/data1/fmt_ref/human_g1k_v37_decoy.fasta
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#out=new-wgs.sam
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out=/dev/null
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time ./fastbwa 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 -2 #> seed.txt #-Z
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