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I'm trying to run HaplotypeCaller on a haploid organism. Is this possible? What argument should I use for this?
My first attempt produced a diploid calls.
Sorry for the silly question
Currently the HaplotypeCaller only supports diploid calling. If you want to call non-diploid samples you'll need to use the UnifiedGenotyper.
Geraldine Van der Auwera, PhD
Geraldine, I wonder whether the Broad production pipelines processes sex chromosomes in male samples different than autosomes or sex chromosomes in female samples? I've read you're using both UG and HC, so are you ignoring the HC calls (if any)?
We don't currently do anything special with the sex chromosomes in our production pipeline. This means that in male samples, X and Y get called as if they were diploid, so heterozygous calls should be thrown out. As far as I know, any researchers working on the sex chromosomes have their own approaches to dealing with this since it is a fairly specialized topic.
One year after the question, I was wondering if this answer is still true ?
HaplotypeCaller still only supports diploid calling ?
Thanks a lot !
Yes, only diploid still. But we do have plans to work on this in the not too distant future.
Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT
For anyone reading this thread now. HaplotypeCaller now has a --sample_ploidy argument.
is it --sample_ploidy or -ploidy for HC inorder to use it for Haploid Organism..Please reply ASAP
You can use either. https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php#--sample_ploidy
@kshitij_tandon Please think about how it sounds when you ask for a reply "ASAP". Think about how many people are asking questions, and how it's likely that most of them are waiting for an answer in order to be able to move on with their work. In that context, do you think that asking for a reply "ASAP" will get you priority service? Do you think it should?
Just to confirm. In case of Haploid organism argument for variant calling with Haplotype caller will involve '-ploidy 1'.??