Joint derived allele counts of annotated Emperor and King penguin genomic variants with transcription coverage

Joint derived allele counts for King and Emperor penguin samples using Adelie and Gentoo penguins samples as outgroups. The resulting summary table (daf.joint.no00.rnaCov included the following information: 
- counts of derived alleles and total alleles in Emperor penguin (Der1; Tot1), King penguin (Der2; Tot2), and Adélie and Gentoo penguins (Der_out; Tot_out) samples; 
- average allele coverage (avgCov); 
- ancestral (Ref) and derived (Alt) allele; 
- genomic site type (Vartype) based on the first annotation by SNPeff as missense if containing the word ‘missense’, synonymous if containing the word ‘synonymous’, intergenic if containing the word ‘intergenic’, intronic if containing the word ‘intron’, else otherwise;
- genomic site predicted effect (effect) based on the the first annotation description as HIGH, MODERATE, LOW, MODIFIER;
- a flag whether the polymorphic site was originally called as MNP or SNP by freebayes (FlagQual: haplo, snp);
- a flag to track how the derived allele was called (FlagPol) on the basis of the options shown in Supplementary Figure 1 of the related manuscript.
- RNA coverage counts per base for Emperor and King penguins (KingRnaCov, EmpRnaCov