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Jump to navigationJump to searchTutorial: EMMAX GotCloud STOM: Lecture 8 (view source)
Revision as of 20:00, 6 January 2014
, 20:00, 6 January 2014→Run Single Variant Analysis
* Look at your score
* Look at your score
head = ~/out/assoc/single.b.score.epacts.top5000�
head = ~/out/assoc/single.b.score.epacts.top5000
* Variant annotation with EPACTS
* Variant annotation with EPACTS
$S5/epacts/bin/epacts anno --in ~/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz --out ~/out/snps/chr7.filtered.PASS.beagled.anno.vcf.gz --ref $S5/examples/chr7Ref/hs37d5.chr7.fa
$S5/epacts/bin/epacts anno --in ~/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz --out ~/out/snps/chr7.filtered.PASS.beagled.anno.vcf.gz --ref $S5/examples/chr7Ref/hs37d5.chr7.fa
=== Visualizing Zoom Plot ====
* Use ENCODE GM12878 cell type to diplsy variants in the locusZoom-like plot
$S5/epacts/bin/epacts-zoom --vcf ~/out/snps/chr7.filtered.PASS.beagled.anno.vcf.gz --pos 7:117149147 --prefix ~/out/assoc/single.b.score --cellType Gm12878
Copy the output file single.b.score.zoom.7.117149147.pdf using WinSCP or other file transfer software
=== Run Groupwise Test ===
=== Run Groupwise Test ===
