Im using the mpileup application on galaxy and every base is being called with the ALT <x>. It has 110,000,000 lines as well which seems to be too much. I'm just trying to call SNPs and INDELS. Here is a screenshot. https://gyazo.com/f70ca31ebd7d47421b4e702ae3cb91f3 Does anybody know what I am doing wrong?
This prior post at Biostars.org has help for the same issue: https://www.biostars.org/p/161981/. See Devon's reply (currently the second answer).
In Galaxy: When using MPilieup, output BCF (instead of VCF) then convert to VCF excluding non-ATGC bases with the tool bcftools view.
Hopefully this helps! Jen, Galaxy team