RVS

Robust Variance Score.

The robust variance score (RVS) is a novel likelihood-based method for genetic association with NGS data from external control groups. RVS substitutes genotype calls by their expected values given observed sequence data and implements a robust variance estimate for the score statistic.

Reference:

Derkach, A et al.
Association Analysis Using Next Generation Sequence Data from Publicly Available Control Groups: The Robust Variance Score Statistic.
Bioinformatics 30 (15): 2179-2188 first published online April 14, 2014. PMID:24733292

R code

  1. RVS.rar contains the following files, as of Mar 5, 2014:


  2. Oct 27, 2014: R package core functions release: RVS at github.com.

  3. Nov 10, 2014: RVS example for NULL case using 1000 snps:

    • RVS core R package (same version on github as of Oct 27, 2014): rvs_0.0.tar.gz.

    • Example R code for the NULL (no association) case: example_new_NULL.r
      • Refer to pg 2182 (section 2.3.1 of publication referenced above)

    • Test vcf inputfile containing 1000 snps: 1g113low_1g56exomehigh_filtered.hg19.chr11_1000snps.vcf.

    • Test bam inputfile containing IDs for the cases: bam.

    • Notes: First download and install RVS and then run example file:
      1. install.packages("rvs_0.0.tar.gz")
      2. R --no-save < example_new_NULL.r






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