Changes

From Genome Analysis Wiki
Jump to navigationJump to search

SeqShop: Genetic Association Analysis Practical, June 2014 (view source)

Revision as of 02:51, 19 June 2014

536 bytes added ,  02:51, 19 June 2014
→‎Annotating Variants with EPACTS
Line 184: Line 184:  
* How can you represent the variant in terms of amino acid changes?
 
* How can you represent the variant in terms of amino acid changes?
   −
=== Run Single Variant Analysis ===
+
== Single Variant Association Analysis ==
   −
* Run 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
   −
  mkdir ~/out/assoc
+
  head $OUT/assoc/single.epacts.top5000
−
$S5/epacts/bin/epacts single --ped $S5/examples/index/chr7.CFTR.ped --vcf ~/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz --pheno PHENO --out ~/out/assoc/single.b.score --test b.score --anno --ref $S5/examples/chr7Ref/hs37d5.chr7.fa --region 7:117000000-117500000 --run 1
     −
* Look at the association statistics
+
#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
−
  head ~/out/assoc/single.b.score.epacts.top5000
+
  22 36993088 36993088 22:36993088_G/C 62 30 1 0.24194 7.3258e-07 4.9525 31 31 0.43548 0.048387
−
 
+
22 36997871 36997871 22:36997871_G/T 62 30 1 0.24194 7.3258e-07 4.9525 31 31 0.43548 0.048387
−
* Variant annotation with EPACTS
+
22 36987368 36987368 22:36987368_G/A 62 31 1 0.25 2.0898e-06 4.7445 31 31 0.43548 0.064516
−
 
+
22 36987861 36987861 22:36987861_A/G 62 31 1 0.25 2.0898e-06 4.7445 31 31 0.43548 0.064516
−
  $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
+
  22 36985499 36985499 22:36985499_C/T 62 29 1 0.23387 5.7389e-06 4.5358 31 31 0.40323 0.064516
 +
22 36978260 36978260 22:36978260_G/T 62 28 1 0.22581 1.5051e-05 4.3279 31 31 0.3871 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 36667082 36667082 22:36667082_T/G 62 28 1 0.22581 0.0003506 -3.5747 31 31 0.080645 0.37097
    
=== Visualizing Zoom Plot ===
 
=== Visualizing Zoom Plot ===
Line 207: Line 209:  
Copy the output file single.b.score.zoom.7.117149147.pdf using WinSCP or other file transfer software
 
Copy the output file single.b.score.zoom.7.117149147.pdf using WinSCP or other file transfer software
   −
=== Run Groupwise Test ===
+
== Run Groupwise Test ==
    
* Create a set of markers to test
 
* Create a set of markers to test
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/10994"

Navigation menu