Line 108: |
Line 108: |
| NA06984.recal.bam NA06984.recal.bam.bai.done NA06984.recal.bam.metrics NA12878.recal.bam NA12878.recal.bam.bai.done NA12878.recal.bam.metrics | | NA06984.recal.bam NA06984.recal.bam.bai.done NA06984.recal.bam.metrics NA12878.recal.bam NA12878.recal.bam.bai.done NA12878.recal.bam.metrics |
| NA06984.recal.bam.bai NA06984.recal.bam.done NA06984.recal.bam.qemp NA12878.recal.bam.bai NA12878.recal.bam.done NA12878.recal.bam.qemp | | NA06984.recal.bam.bai NA06984.recal.bam.done NA06984.recal.bam.qemp NA12878.recal.bam.bai NA12878.recal.bam.done NA12878.recal.bam.qemp |
| + | |
| + | You can view the aligned sequence reads by running |
| + | % samtools view align/bams/NA06984.recal.bam | less |
| | | |
| Examine the QC metrics by | | Examine the QC metrics by |
Line 434: |
Line 437: |
| 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 |
| + | Successfully written phenotypes and 0 covariates across 99 individuals |
| + | Processing chromosome 7... |
| + | Finished generating EPACTS Makefile |
| + | Running 1 parallel jobs of EPACTS |
| + | make -f /home/presenter02/test.v1/assoc/single.b.score.Makefile -j 1 |
| + | Loading required package: epactsR |
| + | Sucessfully wrote ( 1388 * 10 ) matrix |
| + | The following parameters are available. Ones with "[]" are in effect: |
| + | |
| + | Available Options |
| + | Required Parameters : |
| + | -i [/home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts] |
| + | -o [/home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp] |
| + | Gene Annotation |
| + | Parameters : -g [/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/hg19_gencodeV14.txt.gz] |
| + | -r [/home/presenter02/day2/session1/uwcmg_2013_08//examples/chr7Ref/hs37d5.chr7.fa] |
| + | --inputFormat [epacts], --checkReference, -f [refGene] |
| + | -p [/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/priority.txt] |
| + | -c [/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/codon.txt] |
| + | -u [], -d [], --se [], --si [], --outputFormat [] |
| + | Other Annotation Tools : --genomeScore [], --bed [], --tabix [] |
| + | Load reference genome /home/presenter02/day2/session1/uwcmg_2013_08//examples/chr7Ref/hs37d5.chr7.fa... |
| + | DONE: 1 chromosomes and 159138663 bases are loaded. |
| + | Load codon file /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/codon.txt... |
| + | DONE: codon file loaded. |
| + | Load priority file /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/priority.txt... |
| + | DONE: 24 priority annotation types loaded. |
| + | Load gene file /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/hg19_gencodeV14.txt.gz... |
| + | DONE: 92627 gene loaded. |
| + | DONE: Generated frequency of each annotype type in [ /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp.anno.frq ]. |
| + | 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 ]. |
| + | Ts/Tv ratio: 2.02397 |
| + | Ts observed: 929 times; Tv observed: 459 times. |
| + | DONE: Generated frequency of each base change in [ /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp.base.frq ]. |
| + | DONE: Generated frequency of each codon change in [ /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp.codon.frq ]. |
| + | DONE: Generated frequency of indel length in [ /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp.indel.frq ]. |
| + | nsnps = 866 |
| + | 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 |
| + | NULL |
| + | NULL |
| + | /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 |
| + | /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 |
| + | .............................................. |
| + | ... Anno(tation) ... |
| + | ... Xiaowei Zhan, Goncalo Abecasis ... |
| + | ... Speical Thanks: ... |
| + | ... Hyun Ming Kang, Yanming Li ... |
| + | ... zhanxw@umich.edu ... |
| + | ... Sep 2011 ... |
| + | ................................................ |
| + | |
| + | DONE: 1388 varaints are annotated. |
| + | DONE: Generated annotation output in [ /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts.tmp ]. |
| + | Annotation succeed! |
| + | 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 |
| + | 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 |
| + | /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 |
| + | /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//bin/tabix -f -pbed /home/presenter02/test.v1/assoc/single.b.score.epacts.gz |
| + | rm -f /home/presenter02/test.v1/assoc/single.b.score.7.117000000.117500000.epacts |
| + | /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 |
| + | Rscript /home/presenter02/test.v1/assoc/single.b.score.epacts.R --vanilla |
| + | |
| + | 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 |
| + | 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=$PATH:/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../bin/epstopdf /home/presenter02/test.v1/assoc/single.b.score.epacts.qq.eps |
| + | export GDFONTPATH=/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../share/EPACTS; export GNUPLOT_FONTPATH=/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../share/EPACTS; export GNUPLOT_PS_DIR=/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../share/EPACTS; export PATH=$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 |
| + | 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 |
| + | 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 |
| + | zcat /home/presenter02/test.v1/assoc/single.b.score.epacts.gz | awk '$9 != "NA" { print $0 }' | sort -g -k 9 | head -n 5000 > /home/presenter02/test.v1/assoc/single.b.score.epacts.top5000 |
| + | touch /home/presenter02/test.v1/assoc/single.b.score.epacts.OK |
| + | d-69-91-154-62:~ hmkang$ cat tmp.txt | perl -lane 's/test\.v1/test/g; print " $_"' |
| + | uccessfully written phenotypes and 0 covariates across 99 individuals |
| + | Processing chromosome 7... |
| + | Finished generating EPACTS Makefile |
| + | Running 1 parallel jobs of EPACTS |
| + | make -f /home/presenter02/test/assoc/single.b.score.Makefile -j 1 |
| + | Loading required package: epactsR |
| + | Sucessfully wrote ( 1388 * 10 ) matrix |
| + | The following parameters are available. Ones with "[]" are in effect: |
| + | |
| + | Available Options |
| + | Required Parameters : |
| + | -i [/home/presenter02/test/assoc/single.b.score.7.117000000.117500000.epacts] |
| + | -o [/home/presenter02/test/assoc/single.b.score.7.117000000.117500000.epacts.tmp] |
| + | Gene Annotation |
| + | Parameters : -g [/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/hg19_gencodeV14.txt.gz] |
| + | -r [/home/presenter02/day2/session1/uwcmg_2013_08//examples/chr7Ref/hs37d5.chr7.fa] |
| + | --inputFormat [epacts], --checkReference, -f [refGene] |
| + | -p [/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/priority.txt] |
| + | -c [/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/codon.txt] |
| + | -u [], -d [], --se [], --si [], --outputFormat [] |
| + | Other Annotation Tools : --genomeScore [], --bed [], --tabix [] |
| + | Load reference genome /home/presenter02/day2/session1/uwcmg_2013_08//examples/chr7Ref/hs37d5.chr7.fa... |
| + | DONE: 1 chromosomes and 159138663 bases are loaded. |
| + | Load codon file /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/codon.txt... |
| + | DONE: codon file loaded. |
| + | Load priority file /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/priority.txt... |
| + | DONE: 24 priority annotation types loaded. |
| + | Load gene file /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/hg19_gencodeV14.txt.gz... |
| + | DONE: 92627 gene loaded. |
| + | DONE: Generated frequency of each annotype type in [ /home/presenter02/test/assoc/single.b.score.7.117000000.117500000.epacts.tmp.anno.frq ]. |
| + | DONE: Generated frequency of each highest priority annotation type in [ /home/presenter02/test/assoc/single.b.score.7.117000000.117500000.epacts.tmp.top.anno.frq ]. |
| + | Ts/Tv ratio: 2.02397 |
| + | Ts observed: 929 times; Tv observed: 459 times. |
| + | DONE: Generated frequency of each base change in [ /home/presenter02/test/assoc/single.b.score.7.117000000.117500000.epacts.tmp.base.frq ]. |
| + | DONE: Generated frequency of each codon change in [ /home/presenter02/test/assoc/single.b.score.7.117000000.117500000.epacts.tmp.codon.frq ]. |
| + | DONE: Generated frequency of indel length in [ /home/presenter02/test/assoc/single.b.score.7.117000000.117500000.epacts.tmp.indel.frq ]. |
| + | nsnps = 866 |
| + | 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/assoc/single.b.score.phe NULL /home/presenter02/test/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/assoc/single.b.score.7.117000000.117500000.epacts GT 1e-06 1 3 1000000000 0.5 0 FALSE single.b.score |
| + | NULL |
| + | NULL |
| + | /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//bin/epacts-anno --in /home/presenter02/test/assoc/single.b.score.7.117000000.117500000.epacts --ref /home/presenter02/day2/session1/uwcmg_2013_08//examples/chr7Ref/hs37d5.chr7.fa |
| + | /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//bin/anno -i /home/presenter02/test/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/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 |
| + | .............................................. |
| + | ... Anno(tation) ... |
| + | ... Xiaowei Zhan, Goncalo Abecasis ... |
| + | ... Speical Thanks: ... |
| + | ... Hyun Ming Kang, Yanming Li ... |
| + | ... zhanxw@umich.edu ... |
| + | ... Sep 2011 ... |
| + | ................................................ |
| + | |
| + | DONE: 1388 varaints are annotated. |
| + | DONE: Generated annotation output in [ /home/presenter02/test/assoc/single.b.score.7.117000000.117500000.epacts.tmp ]. |
| + | Annotation succeed! |
| + | mv /home/presenter02/test/assoc/single.b.score.7.117000000.117500000.epacts.tmp /home/presenter02/test/assoc/single.b.score.7.117000000.117500000.epacts |
| + | rm /home/presenter02/test/assoc/single.b.score.7.117000000.117500000.epacts.tmp.log /home/presenter02/test/assoc/single.b.score.7.117000000.117500000.epacts.tmp.top.anno.frq /home/presenter02/test/assoc/single.b.score.7.117000000.117500000.epacts.tmp.anno.frq /home/presenter02/test/assoc/single.b.score.7.117000000.117500000.epacts.tmp.base.frq /home/presenter02/test/assoc/single.b.score.7.117000000.117500000.epacts.tmp.codon.frq /home/presenter02/test/assoc/single.b.score.7.117000000.117500000.epacts.tmp.indel.frq |
| + | /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//bin/epacts-cat /home/presenter02/test/assoc/single.b.score.7.117000000.117500000.epacts | /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//bin/bgzip -c > /home/presenter02/test/assoc/single.b.score.epacts.gz |
| + | /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//bin/tabix -f -pbed /home/presenter02/test/assoc/single.b.score.epacts.gz |
| + | rm -f /home/presenter02/test/assoc/single.b.score.7.117000000.117500000.epacts |
| + | /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//bin/epacts-plot --in /home/presenter02/test/assoc/single.b.score.epacts.gz --region 7:0 |
| + | Rscript /home/presenter02/test/assoc/single.b.score.epacts.R --vanilla |
| + | |
| + | 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/assoc/single.b.score.epacts.cmd |
| + | 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=$PATH:/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../bin/epstopdf /home/presenter02/test/assoc/single.b.score.epacts.qq.eps |
| + | export GDFONTPATH=/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../share/EPACTS; export GNUPLOT_FONTPATH=/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../share/EPACTS; export GNUPLOT_PS_DIR=/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../share/EPACTS; export PATH=$PATH:/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/../bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /home/presenter02/test/assoc/single.b.score.epacts.cmd |
| + | 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/assoc/single.b.score.epacts.mh.eps |
| + | rm /home/presenter02/test/assoc/single.b.score.epacts.cmd /home/presenter02/test/assoc/single.b.score.epacts.qq.eps /home/presenter02/test/assoc/single.b.score.epacts.mh.eps /home/presenter02/test/assoc/single.b.score.epacts.*.dat |
| + | zcat /home/presenter02/test/assoc/single.b.score.epacts.gz | awk '$9 != "NA" { print $0 }' | sort -g -k 9 | head -n 5000 > /home/presenter02/test/assoc/single.b.score.epacts.top5000 |
| + | touch /home/presenter02/test/assoc/single.b.score.epacts.OK |
| + | |
| + | To examine the top signals of association, try |
| + | |
| + | % head assoc/single.b.score.epacts.top5000 |
| + | #CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE NS.CASE NS.CTRL AF.CASE AF.CTRL |
| + | 7 117130755 117130755 7:117130755_C/G_Intron:CFTR 99 9 1 0.045455 0.0018407 3.1148 50 49 0.09 0 |
| + | 7 117149147 117149147 7:117149147_G/A_Nonsynonymous:CFTR 99 9 1 0.045455 0.0018407 3.1148 50 49 0.09 0 |
| + | 7 117120141 117120141 7:117120141_G/C_Utr5:CFTR 99 14 1 0.070707 0.0034417 -2.9253 50 49 0.02 0.12245 |
| + | 7 117356483 117356483 7:117356483_C/T_Intron:CTTNBP2 99 11 1 0.055556 0.0035695 -2.9139 50 49 0.01 0.10204 |
| + | 7 117459023 117459023 7:117459023_A/G_Intron:CTTNBP2 99 121 1 0.38889 0.0047674 2.8223 5049 0.71 0.5102 |
| + | 7 117430909 117430909 7:117430909_T/C_Intron:CTTNBP2 99 10 1 0.050505 0.0068926 -2.702 50 49 0.01 0.091837 |
| + | 7 117456904 117456904 7:117456904_C/T_Intron:CTTNBP2 99 115 1 0.41919 0.0076959 2.6651 5049 0.68 0.47959 |
| + | 7 117457141 117457141 7:117457141_G/C_Intron:CTTNBP2 99 115 1 0.41919 0.0076959 2.6651 5049 0.68 0.47959 |
| + | 7 117467003 117467003 7:117467003_T/A_Intron:CTTNBP2 99 122 1 0.38384 0.0077344 2.6634 5049 0.71 0.52041 |
| + | |
| + | Also you can examine the PDF output file (although it is a tiny fraction of genome), if your X11 works. |
| + | |
| + | % xpdf assoc/single.b.score.epacts.qq.pdf |
| + | % xpdf assoc/single.b.score.epacts.mh.pdf |
| + | |
| + | Running variant annotation using EPACTS is also possible |
| | | |
| % 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 |
| + | /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//bin/anno -i /home/presenter02/day2/session1/uwcmg_2013_08//out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz -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 snps/chr7.filtered.PASS.beagled.anno.vcf.gz --inputFormat vcf -p /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/priority.txt |
| + | The following parameters are available. Ones with "[]" are in effect: |
| + | |
| + | Available Options |
| + | Required Parameters : |
| + | -i [/home/presenter02/day2/session1/uwcmg_2013_08//out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz] |
| + | -o [snps/chr7.filtered.PASS.beagled.anno.vcf.gz] |
| + | Gene Annotation |
| + | Parameters : -g [/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/hg19_gencodeV14.txt.gz] |
| + | -r [/home/presenter02/day2/session1/uwcmg_2013_08/examples/chr7Ref/hs37d5.chr7.fa] |
| + | --inputFormat [vcf], --checkReference, -f [refGene] |
| + | -p [/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/priority.txt] |
| + | -c [/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/codon.txt] |
| + | -u [], -d [], --se [], --si [], --outputFormat [] |
| + | Other Annotation Tools : --genomeScore [], --bed [], --tabix [] |
| + | Load reference genome /home/presenter02/day2/session1/uwcmg_2013_08/examples/chr7Ref/hs37d5.chr7.fa... |
| + | DONE: 1 chromosomes and 159138663 bases are loaded. |
| + | Load codon file /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/codon.txt... |
| + | DONE: codon file loaded. |
| + | Load priority file /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/priority.txt... |
| + | DONE: 24 priority annotation types loaded. |
| + | Load gene file /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/hg19_gencodeV14.txt.gz... |
| + | DONE: 92627 gene loaded. |
| + | DONE: Generated frequency of each annotype type in [ snps/chr7.filtered.PASS.beagled.anno.vcf.gz.anno.frq ]. |
| + | DONE: Generated frequency of each highest priority annotation type in [ snps/chr7.filtered.PASS.beagled.anno.vcf.gz.top.anno.frq ]. |
| + | Ts/Tv ratio: 2.02397 |
| + | Ts observed: 929 times; Tv observed: 459 times. |
| + | DONE: Generated frequency of each base change in [ snps/chr7.filtered.PASS.beagled.anno.vcf.gz.base.frq ]. |
| + | DONE: Generated frequency of each codon change in [ snps/chr7.filtered.PASS.beagled.anno.vcf.gz.codon.frq ]. |
| + | DONE: Generated frequency of indel length in [ snps/chr7.filtered.PASS.beagled.anno.vcf.gz.indel.frq ]. |
| + | .............................................. |
| + | ... Anno(tation) ... |
| + | ... Xiaowei Zhan, Goncalo Abecasis ... |
| + | ... Speical Thanks: ... |
| + | ... Hyun Ming Kang, Yanming Li ... |
| + | ... zhanxw@umich.edu ... |
| + | ... Sep 2011 ... |
| + | ................................................ |
| + | |
| + | DONE: 1388 varaints are annotated. |
| + | DONE: Generated annotation output in [ snps/chr7.filtered.PASS.beagled.anno.vcf.gz ]. |
| + | Annotation succeed! |
| + | mv snps/chr7.filtered.PASS.beagled.anno.vcf.gz /home/presenter02/day2/session1/uwcmg_2013_08//out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz.tmp |
| + | /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//bin/bgzip -c /home/presenter02/day2/session1/uwcmg_2013_08//out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz.tmp > snps/chr7.filtered.PASS.beagled.anno.vcf.gz |
| + | /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//bin/tabix -pvcf -f snps/chr7.filtered.PASS.beagled.anno.vcf.gz |
| + | rm /home/presenter02/day2/session1/uwcmg_2013_08//out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz.tmp |
| + | rm snps/chr7.filtered.PASS.beagled.anno.vcf.gz.log snps/chr7.filtered.PASS.beagled.anno.vcf.gz.top.anno.frq snps/chr7.filtered.PASS.beagled.anno.vcf.gz.anno.frq snps/chr7.filtered.PASS.beagled.anno.vcf.gz.base.frq snps/chr7.filtered.PASS.beagled.anno.vcf.gz.codon.frq snps/chr7.filtered.PASS.beagled.anno.vcf.gz.indel.frq |
| + | |
| + | You can look at example non-synonymous SNPs. |
| | | |
| % 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 |
| + | |
| + | The following examples running gene-level burden test (skipped for the workshop),for your record. |
| | | |
| % ${GC}/epacts/bin/epacts make-group --vcf snps/chr7.filtered.PASS.beagled.anno.vcf.gz --out snps/chr7.filtered.PASS.beagled.anno.grp –nonsyn | | % ${GC}/epacts/bin/epacts make-group --vcf snps/chr7.filtered.PASS.beagled.anno.vcf.gz --out snps/chr7.filtered.PASS.beagled.anno.grp –nonsyn |
Line 449: |
Line 663: |
| == STEP 5 : All-in-one running of all scripts (for later use) == | | == STEP 5 : All-in-one running of all scripts (for later use) == |
| | | |
− | % tar xzvf /home/presenter02/day2/session1/uwcmg_2013_08.tar.gz� | + | % tar xzvf /home/presenter02/day2/session1/uwcmg_2013_08.tar.gz |
| | | |
− | % cd /home/presenter02/day2/session1/uwcmg_2013_08� | + | % cd /home/presenter02/day2/session1/uwcmg_2013_08 |
| | | |
− | % sh go.sh � | + | % sh go.sh |