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Calling complex pedigrees with HaplotypeCaller
I want to use HaplotypeCaller to call families together. I have bam files for each individual in the 4 families I am studying, as well as a ped file describing the pedigree information. The problem is that these families have complex pedigrees, with the parents (mother and father), the children, and then one grandchild for each child (do not have information about the other parent of the grandchild). I would like to call these families with their complex pedigrees together, and I would like to call all the 4 families together to maximize the power of the calling. However, I'm not sure how to do that with just the -ped option. -ped seems to be designed for only one family or cohort, and I'm not sure it would work for me to feed it all my bams as inputs. Are there any other tools for GATK that I could use to call complex pedigrees?
The other possibility would be to call the 4 trios separately and each child-grandchild pair separately, but not sure how to do that either with just -ped. What would you recommend?
And finally, I get an error message saying that --emitRefConfidence only works for single sample mode. It seems that I should omit this option when I run HaplotypeCaller on my families, but are there any other options that I should use for cohort calling besides the standard ones (which I know to be --variant_index_type and --variant_index_parameter)?