Has anyone tried to make indel calls from haploid data using UnifiedGenotyper?
At the moment, I am not sure running the default parameters in this situation is the best practice. My first thought was to adjust the --heterozygosity and --indel_heterozygosity parameters to 0. However, this resulted in no calls being made whatsoever when I tried it with -glm INDEL.
There is another thread with a similar question to this topic here:
But, I would like to know about the GATK UnifiedGenotyper in particular for this haploid situation.
At the moment, I am not sure running the default parameters in this situation is the best practice. My first thought was to adjust the --heterozygosity and --indel_heterozygosity parameters to 0. However, this resulted in no calls being made whatsoever when I tried it with -glm INDEL.
There is another thread with a similar question to this topic here:
But, I would like to know about the GATK UnifiedGenotyper in particular for this haploid situation.
