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Association analyses were performed using the plink genetic analysis toolset, with adjustment for relevant covariates.
The whole genome association analysis toolset (PLINK) was used for association analysis at the allelic level [27].
plink (http://pngu.mgh.harvard.edu/∼purcell/plink) is a free, open-source whole-genome association analysis toolset, which efficiently performs association studies for single SNPs or computationally intensive genome-wide association studies.
We trimmed the raw reads using the 'nesoni clip' tool from the Nesoni high-throughput sequencing data analysis toolset (Version 0.114, http://www.vicbioinformatics.com/software.nesoni.shtml) for Illumina adapters and a minimum quality of 2. Additionally, we removed the first 9 and last 5 bases from each read.
Data analysis was performed in the Fluidigm Singular Analysis Toolset 3.0 in R. See Supplemental Experimental Procedures and Supplemental Theory for all details of model construction.
All tests involving our primary endpoints were performed using PLINK, a free, open-source genetic analysis toolset (http://pngu.mgh.harvard.edu/purcell/plink/) [33].
All association tests and permutations were performed using the PLINK software (v1.0.6), an open-source whole genome association analysis toolset [41], available at http://pngu.mgh.harvard.edu/purcell/plink/.
PLINK is a commonly used whole-genome association analysis toolset.
Quality control was carried out using the PLINK v1.07 whole genome association analysis toolset [ 24].
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