216
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
This is the typical DIAGRAM analysis using your current association pipeline and software. [[Image:1000Genomes march2012 imputation analysis plan 08312012.pdf]]
This is the typical DIAGRAM analysis using your current association pipeline and software. [[Image:1000Genomes march2012 imputation analysis plan 08312012.pdf]]
==== Alternative: Analyze VCF and PED files using the Wald test ====
==== Alternative: Analyze VCF and PED files using the Wald test with the EPACTS software: ====
This will be a good way to check if your VCF and PED files are correctly formatted for EPACTS.
<pre>epacts.v2.2.0.20121026 /epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \
-test b.wald -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -field EC -run 10
</pre>
'''Important:''' To analyze dosages (not genotypes), you must specify the dosage field with the "--field EC" option. Without this option, you will be analyzing the hard genotypes (i.e. --field option defaults to "GT" or "genotypes")!
=== 2. Analysis of low frequency variants using Firth bias-corrected logistic regression ===
=== 2. Analysis of low frequency variants using Firth bias-corrected logistic regression ===
To run the Firth test using the EPACTS software:
To run the Firth test using the EPACTS software:
<pre>epacts2.1/epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \
<pre>epacts.v2.2.0.20121026 /epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \
-test b.firth -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -max-mac 200 -field EC -run 10
-test b.firth -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -max-mac 200 -field EC -run 10
</pre>
</pre>
The EPACTS command for the score test analysis of chromosome 20 is:
The EPACTS command for the score test analysis of chromosome 20 is:
<pre>epacts2.1/epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \
<pre>epacts.v2.2.0.20121026 /epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \
-test b.score -pheno DISEASE -cov AGE -chr 20 -anno -min-mac 1 -field EC -run 10
-test b.score -pheno DISEASE -cov AGE -chr 20 -anno -min-mac 1 -field EC -run 10
</pre>
</pre>
