15 lines
414 B
Bash
15 lines
414 B
Bash
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thread=32
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n_r1=~/fastq/na12878/na12878_r1.fq
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n_r2=~/fastq/na12878/na12878_r2.fq
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#n_r1=~/fastq/ZY2105177532213010_L4_1.fq
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#n_r2=~/fastq/ZY2105177532213010_L4_2.fq
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reference=~/reference/ert/human_g1k_v37_decoy.fasta
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out=/dev/null
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time /home/zzh/work/ert-bwa-mem2/bwa-mem2 mem -t $thread -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
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-Z $reference \
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$n_r1 \
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$n_r2 \
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-o $out
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