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

Revision as of 13:54, 9 March 2011

81 bytes added ,  13:54, 9 March 2011
→‎Steps
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  ${BIN}/samtools-hybrid view  ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam | less
 
  ${BIN}/samtools-hybrid view  ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam | less
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TYPE 'q' to finish
    
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 glfview ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.glf | less
 
  ${BIN}/samtools-hybrid glfview ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.glf | less
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TYPE 'q' to finish
    
10. SINGLE-SAMPLE GENOTYPE CALLING using GLFSINGLE
 
10. SINGLE-SAMPLE GENOTYPE CALLING using GLFSINGLE
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  less ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf
 
  less ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf
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TYPE 'q' to finish
    
11. COMPUTE THE GENOTYPE LIKELIHOOD OF HIGH-COVERAGE DATA  
 
11. COMPUTE THE GENOTYPE LIKELIHOOD OF HIGH-COVERAGE DATA  
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  less ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf
 
  less ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf
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TYPE 'q' to finish
    
13. COUNT NUMBER OF SNPs and OVERLAPS  
 
13. COUNT NUMBER OF SNPs and OVERLAPS  
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/3037"

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