aDNA_GenoCaller is a python program that calls genotypes from bam files at positions/regions specified in a bed file while taking into account post mortem damage as estimate by MapDamage (currently 1.0)
This version of the program will take any genotype with a low quality heterozygote call (Q<30) and convert to the next best homozygote call. pysam and matplotlib libraries in your version of python need to be installed to run the script.
Three files are created: An emit all vcf file noting the call for all base pairs in the bed file. A vcf file with only those sites with evidence for at least one alternative allele and that passes a predetermined QUAL filter. A haploid emit all vcf (ish), that gives you the most likely base under a haploid model. If two or more basepairs are tied, the reported allele is randomly chosen.
To run aDNA_GenoCaller type:
./aDNA_GenoCaller.py indexed_bamfile bed_file reference_genome 5CT_mapdamage_file 3GA_mapdamage_file