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Sequence Analysis Practice 2011/03/09 (view source)

Revision as of 13:43, 9 March 2011

38 bytes added ,  13:43, 9 March 2011
→‎Steps
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== Steps ==
 
== Steps ==
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# SETTING UP ENVIRONMENTAL VARIABLES
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0. SETTING UP ENVIRONMENTAL VARIABLES
    
  setenv BIN /home/hyun/wed/bin2
 
  setenv BIN /home/hyun/wed/bin2
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  mkdir --p ${OUT}
 
  mkdir --p ${OUT}
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# Align using BWA
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1. Align using BWA
    
  ${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
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  ${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
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  ${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
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  ${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 - ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.paired.bwa.sorted
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#. MERGE ALIGNED BAMS INTO A SINGLE BAM
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2. MERGE ALIGNED BAMS INTO A SINGLE BAM
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${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 ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.unpaired.bwa.sorted.bam
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${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
    
3. BRIEF SUMMARY OF THE BAM
 
3. BRIEF SUMMARY OF THE BAM
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${BIN}/samtools-hybrid flagstat ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.merged.bam
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${BIN}/samtools-hybrid flagstat ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.merged.bam
    
4. MARK DUPLICATED READS
 
4. MARK DUPLICATED READS
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${BIN}//superDeDuper -i ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.merged.bam -o ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam -v
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${BIN}//superDeDuper -i ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.merged.bam -o ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam -v
    
5. BRIEF SUMMARY OF THE BAM
 
5. BRIEF SUMMARY OF THE BAM
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${BIN}/samtools-hybrid flagstat ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam
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${BIN}/samtools-hybrid flagstat ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam
    
6. VIEW THE ALIGNMENT
 
6. VIEW THE ALIGNMENT
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${BIN}/samtools-hybrid view  ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam | less
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${BIN}/samtools-hybrid view  ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam | less
    
7. INDEX THE ALIGNMENT FOR RANDOM ACCESS OF THE BAM
 
7. INDEX THE ALIGNMENT FOR RANDOM ACCESS OF THE BAM
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${BIN}/samtools-hybrid index  ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam
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${BIN}/samtools-hybrid index  ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam
    
8. GENOMIC VIEW OF THE ALIGNMENT
 
8. GENOMIC VIEW OF THE ALIGNMENT
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${BIN}/samtools-hybrid tview ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam ${REF}/human_g1k_v37_chr20.fa
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${BIN}/samtools-hybrid tview ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam ${REF}/human_g1k_v37_chr20.fa
    
9. QUALITY CHECKING USING QPLOT
 
9. QUALITY CHECKING USING QPLOT
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${BIN}/qplot --plot ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam.qplot.pdf --stats ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam.qplot.stats --reference ${REF}/human_g1k_v37_chr20.fa --dbsnp ${REF}/dbsnp.b130.ncbi37.chr20.tbl --gccontent ${REF}/ncbi37.chr20.gc ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam
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${BIN}/qplot --plot ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam.qplot.pdf --stats ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam.qplot.stats --reference ${REF}/human_g1k_v37_chr20.fa --dbsnp ${REF}/dbsnp.b130.ncbi37.chr20.tbl --gccontent ${REF}/ncbi37.chr20.gc ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam
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cat ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam.qplot.stats
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cat ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam.qplot.stats
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# xpdf ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam.qplot.pdf
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The PDF file can be viewed  ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam.qplot.pdf
    
9. COMPUTE THE GENOTYPE LIKELIHOOD
 
9. COMPUTE THE GENOTYPE LIKELIHOOD
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/3029"

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