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@Sheila To answer to your questions: * Some samples are paired (one diploid sample paired with one haploid sample). Some others are not (only haploid samples without paired diploid or vice-versa). * I would need the sites to be no-calls only for…
Hi @Geraldine_VdAuwera , For examples, there are samples for which I expect to have the same genotypes at certain sites. Whenever this is not the case, I want to mark the genotypes at those sites as NoCall. For example: s caffold1 159775 . …
(Quote) Hi @Geraldine_VdAuwera , I'm also interested by these additional arguments. Do you know when the next official release will occur roughly ? Thank you very much in advances.
@Sheila Thank you very much ! It's really helpful.
Thank you very much. It works !
Hi, I'm really interested in a detailed documentation on SNP annotation threshold for filtering. If such document exists, could you pleas point us to it? Thank you very much in advance.
Hi Sheila, Thank you for your answers. Finally, I decide to do first the haplotype calling in gVCF mode for all my samples, then do the joint genotyping and the base recalibration so on. I haven't finished yet but this seems not to take that much t…