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, 13:41, 9 March 2011
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| setenv REF /home/hyun/wed/ref2 | | setenv REF /home/hyun/wed/ref2 |
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− | setenv OUT ~/seq/wednesday/output | + | setenv OUT ~/seq/wednesday/output |
− | mkdir --p ${OUT} | + | mkdir --p ${OUT} |
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− | 1. Align using BWA
| + | # Align using BWA |
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− | ${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa ${IN}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read1.fastq.gz > ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read1.fastq.gz.sai | + | ${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa ${IN}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read1.fastq.gz > ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read1.fastq.gz.sai |
− | | + | |
− | ${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa ${IN}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read2.fastq.gz > ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read2.fastq.gz.sai | + | ${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa ${IN}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read2.fastq.gz > ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read2.fastq.gz.sai |
− | | + | |
− | ${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa ${IN}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.unpaired.fastq.gz > ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.unpaired.fastq.gz.sai | + | ${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa ${IN}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.unpaired.fastq.gz > ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.unpaired.fastq.gz.sai |
− | | + | |
− | ${BIN}/bwa samse ${REF}/human_g1k_v37_chr20.fa ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.unpaired.fastq.gz.sai ${IN}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.unpaired.fastq.gz | ${BIN}/samtools-hybrid view -uhS - | ${BIN}/samtools-hybrid sort -m 10000000 - ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.unpaired.bwa.sorted | + | ${BIN}/bwa samse ${REF}/human_g1k_v37_chr20.fa ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.unpaired.fastq.gz.sai ${IN}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.unpaired.fastq.gz | ${BIN}/samtools-hybrid view -uhS - | ${BIN}/samtools-hybrid sort -m 10000000 - ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.unpaired.bwa.sorted |
− | | + | |
− | ${BIN}/bwa sampe ${REF}/human_g1k_v37_chr20.fa ${OUT}//NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read1.fastq.gz.sai ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read2.fastq.gz.sai ${IN}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read1.fastq.gz ${IN}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read2.fastq.gz | ${BIN}/samtools-hybrid view -uhS - | ${BIN}/samtools-hybrid sort -m 10000000 - ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.paired.bwa.sorted | + | ${BIN}/bwa sampe ${REF}/human_g1k_v37_chr20.fa ${OUT}//NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read1.fastq.gz.sai ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read2.fastq.gz.sai ${IN}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read1.fastq.gz ${IN}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read2.fastq.gz | ${BIN}/samtools-hybrid view -uhS - | ${BIN}/samtools-hybrid sort -m 10000000 - ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.paired.bwa.sorted |
− | | + | |
− | 2. MERGE ALIGNED BAMS INTO A SINGLE BAM
| + | #. MERGE ALIGNED BAMS INTO A SINGLE BAM |
| | | |
| ${BIN}/samtools-hybrid merge ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.merged.bam ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.paired.bwa.sorted.bam ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.unpaired.bwa.sorted.bam | | ${BIN}/samtools-hybrid merge ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.merged.bam ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.paired.bwa.sorted.bam ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.unpaired.bwa.sorted.bam |