Changes between Version 17 and Version 18 of SOPs/vcf

Timestamp:

07/27/16 09:55:00 (9 years ago)

Author:

thiruvil

Comment:

--

SOPs/vcf

@@ -86 +86 @@
 * Broad's MutSig ("Mutation Significance")
    * See http://www.broadinstitute.org/cancer/cga/mutsig for details
+
+== Other Analysis ==
+
+* Assess Hardy-Weinberg Equilibrium (HWE) using an exact test,
+  * Use [[https://vcftools.github.io/index.html | vcftools]] option "--hardy" to report a p-value for each site to assess deviation from HWE.  VCF file must have genotypes of individuals explicitly reported.
+{{{
+vcftools --vcf myVariants.vcf --hardy --out myVariantsHWE
+}}}
+  * Alternatively, R package [[https://cran.r-project.org/web/packages/genetics/index.html | genetics]] can be utilized with counts for each genotype,
+{{{
+library(genetics)
+g1 = genotype(c(rep("G/G",1),rep("G/A",47),rep("A/A",6450)))
+HWE.exact(g1)
+}}}
+