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

Revision as of 13:45, 9 March 2011

9 bytes added ,  13:45, 9 March 2011
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  grep -v ^# ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf | wc -l  
 
  grep -v ^# ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf | wc -l  
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cat ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf | grep -v ^# | cut -f 1,2 | sort | uniq -d | wc -l
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 +
cat ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf | grep -v ^# | cut -f 1,2 | sort | uniq -d
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${BIN}/samtools-hybrid tview ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam ${REF}/human_g1k_v37_chr20.fa
 
   
 
   
−
cat ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf | grep -v ^# | cut -f 1,2 | sort | uniq -d | wc -l
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TYPE g , and  20:19989392
−
 
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TYPE g, and  20:20032998
−
cat ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf | grep -v ^# | cut -f 1,2 | sort | uniq -d
  −
 
  −
${BIN}/samtools-hybrid tview ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam ${REF}/human_g1k_v37_chr20.fa
  −
 
  −
type g , and  20:19989392
  −
type g, and  20:20032998
     −
${BIN}/samtools-hybrid tview ${IN}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.bam ${REF}/human_g1k_v37_chr20.fa
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${BIN}/samtools-hybrid tview ${IN}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.bam ${REF}/human_g1k_v37_chr20.fa
    
type g , and  20:19989392
 
type g , and  20:19989392
 
type g, and  20:20032998
 
type g, and  20:20032998
−
      
14. SUMMARIZE STATISTICS
 
14. SUMMARIZE STATISTICS
   −
perl ${BIN}/vcfSummary.pl --vcf ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf --dbsnp ${REF}/dbsnp_129_b37.rod.chr20.map --bfile ${REF}/hapmap3_r3_b37_fwd.consensus.qc.poly.chr20
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perl ${BIN}/vcfSummary.pl --vcf ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf --dbsnp ${REF}/dbsnp_129_b37.rod.chr20.map --bfile ${REF}/hapmap3_r3_b37_fwd.consensus.qc.poly.chr20
−
 
+
−
perl ${BIN}/vcfSummary.pl --vcf ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf --dbsnp ${REF}/dbsnp_129_b37.rod.chr20.map --bfile ${REF}/hapmap3_r3_b37_fwd.consensus.qc.poly.chr20
+
perl ${BIN}/vcfSummary.pl --vcf ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf --dbsnp ${REF}/dbsnp_129_b37.rod.chr20.map --bfile ${REF}/hapmap3_r3_b37_fwd.consensus.qc.poly.chr20
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/3032"

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