41 lines
810 B
Bash
Executable File
41 lines
810 B
Bash
Executable File
thread=128
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n1=~/data/na12878-1.fq.gz
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n2=~/data/na12878-2.fq.gz
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#n1=~/data/dataset/real/D1/1w1.fq
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#n2=~/data/dataset/real/D1/1w2.fq
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#n1=~/data/dataset/real/D1/n1.fq.gz
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#n2=~/data/dataset/real/D1/n2.fq.gz
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#n1=~/data/dataset/real/D2/n1.fq.gz
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#n2=~/data/dataset/real/D2/n2.fq.gz
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#n1=~/data/dataset/real/D3/n1.fq.gz
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#n2=~/data/dataset/real/D3/n2.fq.gz
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#n1=~/data/dataset/real/D4/n1.fq.gz
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#n2=~/data/dataset/real/D4/n2.fq.gz
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#n1=~/data/dataset/real/D5/n1.fq.gz
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#n2=~/data/dataset/real/D5/n2.fq.gz
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reference=~/data/fmt_ref/human_g1k_v37_decoy.fasta
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out=./out.sam
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#out=/dev/null
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sudo /home/zzh/clean_mem.sh
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rm $out
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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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$n1 \
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$n2 \
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-o $out -2 #-Z
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#-K 2560000000 \
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#-K 2100000000
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