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Old 01-24-2012, 08:29 PM   #1
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Default Using UnifiedGenotyper to call variants from haploid data?

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.
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