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Tutorial: GotCloud UW CMG (view source)

Revision as of 05:27, 6 August 2013

60 bytes removed ,  05:27, 6 August 2013
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  % cat ${GC}/examples/index/chr7.CFTR.low_coverage.conf
 
  % cat ${GC}/examples/index/chr7.CFTR.low_coverage.conf
   −
  % time ${GC}/gotcloud/gotcloud snpcall --conf �  ${GC}/examples/index/chr7.CFTR.low_coverage.conf �  --outDir snps --baseprefix ${GC}/examples �  --region 7:117000000-117500000 --numjobs 2
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  % time ${GC}/gotcloud/gotcloud snpcall --conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2
    
  % 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
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  % 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
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  % mkdir assoc
 
  % mkdir assoc
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  % time ${GC}/epacts/bin/epacts single�  --ped ${GC}/examples/index/chr7.CFTR.ped �   --vcf ${GC}/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz�  --pheno PHENO --out assoc/single.b.score --test b.score --anno �   --ref ${GC}/examples/chr7Ref/hs37d5.chr7.fa �   --region 7:117000000-117500000 --run 1
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  % time ${GC}/epacts/bin/epacts single  --ped ${GC}/examples/index/chr7.CFTR.ped  --vcf ${GC}/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz  --pheno PHENO --out assoc/single.b.score --test b.score --anno  --ref ${GC}/examples/chr7Ref/hs37d5.chr7.fa  --region 7:117000000-117500000 --run 1
   −
  % time ${GC}/epacts/bin/epacts anno --in ${GC}/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz --out snps/chr7.filtered.PASS.beagled.anno.vcf.gz --ref ${GC}examples/chr7Ref/hs37d5.chr7.fa�
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  % time ${GC}/epacts/bin/epacts anno --in ${GC}/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz --out snps/chr7.filtered.PASS.beagled.anno.vcf.gz --ref ${GC}examples/chr7Ref/hs37d5.chr7.fa
    
  % zcat snps/chr7.filtered.PASS.beagled.anno.vcf.gz | grep Nonsynonymous | grep CFTR | cut -f 1-8 | head -1
 
  % zcat snps/chr7.filtered.PASS.beagled.anno.vcf.gz | grep Nonsynonymous | grep CFTR | cut -f 1-8 | head -1
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  % ${GC}/epacts/bin/epacts group --ped ${GC}/examples/index/chr7.CFTR.ped --vcf snps/chr7.filtered.PASS.beagled.anno.vcf.gz --out assoc/group.skat.o --groupf snps/chr7.filtered.PASS.beagled.anno.grp --test skat --skat-o --run 2
 
  % ${GC}/epacts/bin/epacts group --ped ${GC}/examples/index/chr7.CFTR.ped --vcf snps/chr7.filtered.PASS.beagled.anno.vcf.gz --out assoc/group.skat.o --groupf snps/chr7.filtered.PASS.beagled.anno.grp --test skat --skat-o --run 2
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�
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  % cat assoc/group.skat.o.epacts  
 
  % cat assoc/group.skat.o.epacts  
    
  % ${GC}/epacts/bin/epacts group --ped ${GC}/examples/index/chr7.CFTR.ped --vcf snps/
 
  % ${GC}/epacts/bin/epacts group --ped ${GC}/examples/index/chr7.CFTR.ped --vcf snps/
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�
 
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/7737"

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