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, 17:10, 9 March 2011
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| ${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 | | ${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 |
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− | ${BIN}/bwa samse ${REF}/human_g1k_v37_chr20.fa \ | + | ${BIN}/bwa samse ${REF}/human_g1k_v37_chr20.fa ${OUT}/NA12878.exon.sample.unpaired.fastq.gz.sai ${IN}/NA12878.exon.sample.unpaired.fastq.gz | ${BIN}/samtools-hybrid view -uhS - | ${BIN}/samtools-hybrid sort -m 10000000 - ${OUT}/NA12878.exon.sample.unpaired.bwa.sorted |
− | ${OUT}/NA12878.exon.sample.unpaired.fastq.gz.sai \
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− | ${IN}/NA12878.exon.sample.unpaired.fastq.gz \
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− | | ${BIN}/samtools-hybrid view -uhS - \
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− | | ${BIN}/samtools-hybrid sort -m 10000000 \
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− | - ${OUT}/NA12878.exon.sample.unpaired.bwa.sorted
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− | ${BIN}/bwa sampe ${REF}/human_g1k_v37_chr20.fa \ | + | ${BIN}/bwa sampe ${REF}/human_g1k_v37_chr20.fa ${OUT}//NA12878.exon.sample.read1.fastq.gz.sai ${OUT}/NA12878.exon.sample.read2.fastq.gz.sai ${IN}/NA12878.exon.sample.read1.fastq.gz ${IN}/NA12878.exon.sample.read2.fastq.gz ${BIN}/samtools-hybrid view -uhS - ${BIN}/samtools-hybrid sort -m 10000000 - ${OUT}/NA12878.exon.sample.paired.bwa.sorted |
− | ${OUT}//NA12878.exon.sample.read1.fastq.gz.sai \
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− | ${OUT}/NA12878.exon.sample.read2.fastq.gz.sai \
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− | ${IN}/NA12878.exon.sample.read1.fastq.gz \
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− | ${IN}/NA12878.exon.sample.read2.fastq.gz \
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− | | ${BIN}/samtools-hybrid view -uhS - \
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− | | ${BIN}/samtools-hybrid sort -m 10000000 \
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− | - ${OUT}/NA12878.exon.sample.paired.bwa.sorted
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| 3. Merge multiple BAMs into one | | 3. Merge multiple BAMs into one |