We ensured DNA and RNA data were from a single individual by making SNP calls from RNA-seq results using samtools and bcftools 0.1.19, using the author-recommended protocol, which includes the “Bayesian inference” option. Calls were made only for SNP locations that were assayed on the genotyping chip. Raw variant calls were filtered, as recommended, using the vcfutils.pl varFilter (v0.1.18) option with the maximum depth set to 120 (roughly twice the average read depth). SNP calls from the DNA genotyping were converted to reference forward strand using PLINK. PLINK/Seq (https://atgu.mgh.harvard.edu/plinkseq/) was then used to generate a VCF file by running the fix-strand and write-vcf commands.
