Custom scripts developed for the processing of genome-wide data for Eulemur macaco and Eulemur flavifrons.
File descriptions:
GenerateEmConsensusFromVCF.py: used to generate a consensus sequence with no polymorphic sites and only low-coverage sites masked from an all-sites VCF file generated using the alignment (.bam) of reads from one species to the reference sequence of another species, produced using GATK
vcfutils_mod.pl: contains modified vcf2fq and vcf2fqnonref functions used to generate SNP-inclusive consensuses for E. flavifrons and E. macaco, respectively, from all-sites VCF files generated using GATK
CalculateDiversityAndDivergence.py: used to calculate per-scaffold diversity within and divergence between species, using high quality base pairs from the all-sites VCF files from GATK