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Tutorial: GotCloud UW CMG (view source)

Revision as of 10:30, 6 August 2013

No change in size ,  10:30, 6 August 2013
→‎STEP 3 : Run GotCloud SNP Calling Pipeline
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  % cat ${GC}/out/snps/vcfs/chr7/chr7.filtered.sites.vcf.summary
 
  % cat ${GC}/out/snps/vcfs/chr7/chr7.filtered.sites.vcf.summary
   −
  % time ${GC}/gotcloud/gotcloud beagle--conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2
+
  % time ${GC}/gotcloud/gotcloud beagle --conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2
    
  % samtools tview ${GC}/examples/bams/NA12843.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam ${GC}/examples/chr7Ref/hs37d5.chr7.fa
 
  % samtools tview ${GC}/examples/bams/NA12843.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam ${GC}/examples/chr7Ref/hs37d5.chr7.fa
−
      
== STEP 4 : EPACTS association analysis  ==  
 
== STEP 4 : EPACTS association analysis  ==  
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/7741"

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