I am trying to automate variant calling on human short exons sequenced with Sanger method. I have the ab1 files, and I want to automate the process for clinical geneticists. The program should be free, I understand that is a huge limitation. Also, it needs to register INDELS in addition to SNPs.
I tried working with tracy, and it works fine but fails silently, and fails to index the reference (I have opened github issues for that). TraceTuner doesn't seem to do anything when I use the -het flag, it just outputs the single consensus fasta (no heterozygous calls). They currently work on Sequencher trial version, but this version doesn't do variant calling. Baseling also doesn't mention automated heterozygous calls. Although there are mentions of writing in ambiguous bases which could be a code for a heterozygous, this becomes a problem for INDELs.
Is there a free resource that somebody uses successfully for human diploid data variant calling? Thanks all!