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33 bytes removed
, 17:09, 9 March 2011
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| 2. Align using BWA | | 2. Align using BWA |
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− | ${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa \ | + | ${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa ${IN}/NA12878.exon.sample.read1.fastq.gz > ${OUT}/NA12878.exon.sample.read1.fastq.gz.sai |
− | ${IN}/NA12878.exon.sample.read1.fastq.gz \
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− | > ${OUT}/NA12878.exon.sample.read1.fastq.gz.sai
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− | ${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa \ | + | ${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa ${IN}/NA12878.exon.sample.read2.fastq.gz > ${OUT}/NA12878.exon.sample.read2.fastq.gz.sai |
− | ${IN}/NA12878.exon.sample.read2.fastq.gz \
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− | > ${OUT}/NA12878.exon.sample.read2.fastq.gz.sai
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− | ${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa \ | + | ${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa ${IN}/NA12878.exon.sample.unpaired.fastq.gz ${OUT}/NA12878.exon.sample.unpaired.fastq.gz.sai |
− | ${IN}/NA12878.exon.sample.unpaired.fastq.gz \
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− | > ${OUT}/NA12878.exon.sample.unpaired.fastq.gz.sai
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| ${BIN}/bwa samse ${REF}/human_g1k_v37_chr20.fa \ | | ${BIN}/bwa samse ${REF}/human_g1k_v37_chr20.fa \ |