I am dealing with the SNP data derived from QTL-mapping (F2 progeny + parents) using GBS sequencing approach. Unfortunately, the data are of low-coverage (~5 reads per site) which is not so good considering the fact that F2 progeny is expected to have a high amount of heterozygous positions (~50%).
So I am really looking for the SNP caller (sensible to low-covered heterzygotes) that is preferred to use in such complex situation. Right now I am using GATK, but want to try some more SNP callers that are more accurate in case of low-covered heterozygous. I also wonder if there is a kind of option to make GATK more sensible to heterozygous sites? I also don't want to use GATK since it is more human-related software, while my object is a non-model plant with sequenced genome.
Please recommend some SNP callers as well as papers/protocols used for in cases of QTL-analysis based on low-coverage GBS-sequencing, if you know such.