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Tutorial: GotCloud UW CMG (view source)

Revision as of 16:04, 6 August 2013

8,870 bytes added ,  16:04, 6 August 2013
→‎STEP 4 : EPACTS association analysis
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Run single variant logistic score test.
 
Run single variant logistic score test.
 
  % ${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
 
  % ${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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Successfully written phenotypes and 0 covariates across 99 individuals
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Processing chromosome 7...
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Finished generating EPACTS Makefile
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Running 1 parallel jobs of EPACTS
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make -f /home/presenter02/test.v1/assoc/single.b.score.Makefile -j 1
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Loading required package: epactsR
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Sucessfully wrote ( 1388 * 10 ) matrix
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The following parameters are available.  Ones with "[]" are in effect:
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Available Options
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    Required Parameters :
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                          -i [/home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts]
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                          -o [/home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp]
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          Gene Annotation
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              Parameters : -g [/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/hg19_gencodeV14.txt.gz]
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                          -r [/home/presenter02/day2/session1/uwcmg_2013_08//examples/chr7Ref/hs37d5.chr7.fa]
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                          --inputFormat [epacts], --checkReference, -f [refGene]
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                          -p [/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/priority.txt]
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                          -c [/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/codon.txt]
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                          -u [], -d [], --se [], --si [], --outputFormat []
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  Other Annotation Tools : --genomeScore [], --bed [], --tabix []
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Load reference genome /home/presenter02/day2/session1/uwcmg_2013_08//examples/chr7Ref/hs37d5.chr7.fa...
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DONE: 1 chromosomes and 159138663 bases are loaded.
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Load codon file /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/codon.txt...
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DONE: codon file loaded.
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Load priority file /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/priority.txt...
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DONE: 24 priority annotation types loaded.
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Load gene file /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/hg19_gencodeV14.txt.gz...
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DONE: 92627 gene loaded.
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DONE: Generated frequency of each annotype type in [ /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp.anno.frq ].
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DONE: Generated frequency of each highest priority annotation type in [ /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp.top.anno.frq ].
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Ts/Tv ratio: 2.02397
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Ts observed: 929  times; Tv observed: 459 times.
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DONE: Generated frequency of each base change in [ /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp.base.frq ].
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DONE: Generated frequency of each codon change in [ /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp.codon.frq ].
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DONE: Generated frequency of indel length in [ /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp.indel.frq ].
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nsnps = 866
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Rscript /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/epactsSingle.R --vanilla /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../ /home/presenter02/test.v1/assoc/single.b.score.phe NULL /home/presenter02/test.v1/assoc/single.b.score.ind /home/presenter02/day2/session1/uwcmg_2013_08//out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz 7:117000000-117500000 /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts GT 1e-06 1 3 1000000000 0.5 0 FALSE single.b.score
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NULL
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NULL
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/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//bin/epacts-anno --in /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts --ref /home/presenter02/day2/session1/uwcmg_2013_08//examples/chr7Ref/hs37d5.chr7.fa
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/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//bin/anno -i /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts -r /home/presenter02/day2/session1/uwcmg_2013_08//examples/chr7Ref/hs37d5.chr7.fa -f refGene -g /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/hg19_gencodeV14.txt.gz -c /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/codon.txt -o /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp --inputFormat epacts -p /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/priority.txt
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..............................................       
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  ...      Anno(tation)                      ...     
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  ...      Xiaowei Zhan, Goncalo Abecasis    ...     
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    ...      Speical Thanks:                    ...   
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    ...      Hyun Ming Kang, Yanming Li        ...   
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      ...      zhanxw@umich.edu                    ... 
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      ...      Sep 2011                            ...
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        ................................................
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DONE: 1388 varaints are annotated.
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DONE: Generated annotation output in [ /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp ].
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Annotation succeed!
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mv /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts
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rm /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp.log /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp.top.anno.frq /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp.anno.frq /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp.base.frq /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp.codon.frq /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp.indel.frq
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/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//bin/epacts-cat /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts | /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//bin/bgzip -c > /home/presenter02/test.v1/assoc/single.b.score.epacts.gz
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/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//bin/tabix -f -pbed /home/presenter02/test.v1/assoc/single.b.score.epacts.gz
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rm -f /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts
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/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//bin/epacts-plot --in /home/presenter02/test.v1/assoc/single.b.score.epacts.gz --region 7:0
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Rscript /home/presenter02/test.v1/assoc/single.b.score.epacts.R --vanilla
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export GDFONTPATH=/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../share/EPACTS; export GNUPLOT_FONTPATH=/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../share/EPACTS; export GNUPLOT_PS_DIR=/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../share/EPACTS; export PATH=$PATH:/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /home/presenter02/test.v1/assoc/single.b.score.epacts.cmd
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export GDFONTPATH=/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../share/EPACTS; export GNUPLOT_FONTPATH=/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../share/EPACTS; export GNUPLOT_PS_DIR=/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../share/EPACTS; export PATH=$PATH:/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../bin/epstopdf /home/presenter02/test.v1/assoc/single.b.score.epacts.qq.eps
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export GDFONTPATH=/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../share/EPACTS; export GNUPLOT_FONTPATH=/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../share/EPACTS; export GNUPLOT_PS_DIR=/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../share/EPACTS; export PATH=$PATH:/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /home/presenter02/test.v1/assoc/single.b.score.epacts.cmd
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export GDFONTPATH=/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../share/EPACTS; export GNUPLOT_FONTPATH=/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../share/EPACTS; export GNUPLOT_PS_DIR=/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../share/EPACTS; export PATH=$PATH:/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../bin/epstopdf /home/presenter02/test.v1/assoc/single.b.score.epacts.mh.eps
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rm /home/presenter02/test.v1/assoc/single.b.score.epacts.cmd /home/presenter02/test.v1/assoc/single.b.score.epacts.qq.eps /home/presenter02/test.v1/assoc/single.b.score.epacts.mh.eps /home/presenter02/test.v1/assoc/single.b.score.epacts.*.dat
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zcat /home/presenter02/test.v1/assoc/single.b.score.epacts.gz | awk '$9 != "NA" { print $0 }' | sort -g -k 9 | head -n 5000 > /home/presenter02/test.v1/assoc/single.b.score.epacts.top5000
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touch /home/presenter02/test.v1/assoc/single.b.score.epacts.OK
    
  % 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
 
  % 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
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/7757"

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