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Jump to navigationJump to search→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>epacts2.1/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 -run 10
-test b.firth -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -max-mac 200 -field EC -run 10
</pre>
<br>'''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")!<br>
=== 3. Analysis of chromosome 20 using logistic regression score test ===
=== 3. Analysis of chromosome 20 using logistic regression score test ===
