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Revision as of 12:23, 19 June 2014
, 12:23, 19 June 2014no edit summary
== Single Variant Association Analysis ==
== Single Variant Association Analysis ==
Let's run a single-variant association analysis using a score test.
$EPACTS/bin/epacts-single --ped $IN/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/single --region 22:36000000-37000000 --test b.score --pheno PHENO --run 2
$EPACTS/bin/epacts-single --ped $IN/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/single --region 22:36000000-37000000 --test b.score --pheno PHENO --run 2
After running it, you will see EPACTS output files by looking at
ls $OUT/assoc
The top association results can be viewed by
head $OUT/assoc/single.epacts.top5000
head $OUT/assoc/single.epacts.top5000
<div class="mw-collapsible mw-collapsed" style="width:400px">
View top association results
<div class="mw-collapsible-content" style="width:800px">
#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE NS.CASE NS.CTRL AF.CASE AF.CTRL
#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE NS.CASE NS.CTRL AF.CASE AF.CTRL
22 36995620 36995620 22:36995620_A/G 62 36 1 0.29032 5.6717e-09 5.8262 31 31 0.51613 0.064516
22 36995620 36995620 22:36995620_A/G 62 36 1 0.29032 5.6717e-09 5.8262 31 31 0.51613 0.064516
22 36998907 36998907 22:36998907_C/T 62 61 1 0.49194 0.00015557 -3.782 31 31 0.30645 0.67742
22 36998907 36998907 22:36998907_C/T 62 61 1 0.49194 0.00015557 -3.782 31 31 0.30645 0.67742
22 36667082 36667082 22:36667082_T/G 62 28 1 0.22581 0.0003506 -3.5747 31 31 0.080645 0.37097
22 36667082 36667082 22:36667082_T/G 62 28 1 0.22581 0.0003506 -3.5747 31 31 0.080645 0.37097
</div>
</div>
You can look also visualize the results by QQ-plot and Manhattan plot
=== Visualizing Zoom Plot ===
=== Visualizing Zoom Plot ===
