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Revision as of 17:13, 9 March 2011
, 17:13, 9 March 2011→Steps
zcat ${IN}/NA12878.exon.sample.read1.fastq.gz | head
zcat ${IN}/NA12878.exon.sample.read1.fastq.gz | head
zcat ${IN}/NA12878.exon.sample.read2.fastq.gz | head
zcat ${IN}/NA12878.exon.sample.read2.fastq.gz | head
zcat ${IN}/NA12878.exon.sample.unpaited.fastq.gz | head
zcat ${IN}/NA12878.exon.sample.unpaired.fastq.gz | head
press q to quit
press q to quit
${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
${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
${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
${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
${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
