lets assume we have reference genome and its mapped reads:
ref: ACGTCTTCGTCAATG read1: ACGA read2: ACGA read3: ACGC read4: ACGC
my variant caller should generate something like: het A/C - 50%. Dou you have any experiences with this calling? What caller can handle this problem? I found that some callers just skip this site.
Thank you Zaag for mention. Probably this kind of caller would be best. Is there any other free solution? Did anybody tested bcftools, varscan, freebayes...?
bcftools does not work for this, the other ones I've never used