2024-04-06 15:05:20 +08:00
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thread=64
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2024-04-02 07:42:37 +08:00
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## d1
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2024-04-06 15:05:20 +08:00
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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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#n_r1=~/data/fastq/dataset/na12878_wes_144/45m_r1.fq
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#n_r2=~/data/fastq/dataset/na12878_wes_144/45m_r2.fq
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#n_r1=~/data/fastq/dataset/na12878_wes_144/45mr1.fq.gz
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#n_r2=~/data/fastq/dataset/na12878_wes_144/45mr2.fq.gz
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2024-04-02 07:42:37 +08:00
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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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2024-04-06 16:08:43 +08:00
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#n_r1=~/data/fastq/dataset/na12878_wgs_101/45m_r1.fq
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#n_r2=~/data/fastq/dataset/na12878_wgs_101/45m_r2.fq
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2024-04-02 07:42:37 +08:00
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# d3
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2024-03-27 23:47:39 +08:00
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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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2024-04-06 15:05:20 +08:00
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#n_r1=~/data/fastq/dataset/na12878_wgs_150/45mr1.fq.gz
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#n_r2=~/data/fastq/dataset/na12878_wgs_150/45mr2.fq.gz
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2024-04-02 07:42:37 +08:00
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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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2024-04-06 20:53:42 +08:00
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#n_r1=~/data/fastq/dataset/zy_wes/45mr1.fq.gz
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#n_r2=~/data/fastq/dataset/zy_wes/45mr2.fq.gz
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2024-04-02 07:42:37 +08:00
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## d5
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2024-04-06 15:05:20 +08:00
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#n_r1=~/data/fastq/dataset/zy_wgs/45mr1.fq.gz
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#n_r2=~/data/fastq/dataset/zy_wgs/45mr2.fq.gz
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2024-04-02 07:42:37 +08:00
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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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2024-04-06 20:53:42 +08:00
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n_r1=~/data1/fastq/dataset/zy_wgs/E150010395_L01_690_1.fq
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n_r2=~/data1/fastq/dataset/zy_wgs/E150010395_L01_690_2.fq
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2024-03-24 04:40:09 +08:00
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2024-04-06 15:05:20 +08:00
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reference=~/data1/fmt_ref/human_g1k_v37_decoy.fasta
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2024-04-02 07:42:37 +08:00
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#reference=~/reference/bwa/human_g1k_v37_decoy.fasta
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2024-04-06 15:05:20 +08:00
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#reference=~/data/reference/human_g1k_v37_decoy.fasta
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2023-12-25 11:11:19 +08:00
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2024-04-06 20:53:42 +08:00
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out=~/data1/fast-out.sam
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2023-12-25 11:11:19 +08:00
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2024-04-06 20:53:42 +08:00
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time ./fastbwa mem -t $thread -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
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2024-02-07 22:08:51 +08:00
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$reference \
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$n_r1 \
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$n_r2 \
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2024-03-24 04:40:09 +08:00
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-o $out -2
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2023-12-25 11:11:19 +08:00
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