trialleles

[Nahla Hussien AbouEl Ela]

Using stitch, I have a triallelic snp positions, I tried to normalized to keep it, however, STITCH not accept repeated positions, how to fix it? 

[Robbie Davies]

Hi,

Unfortunately, with the way I wrote the code, STITCH can not handle multi-allelic variants in the proper way. At any given position, you can only impute with the reference allele and a single alternate allele. As such, you may want to choose the alternate allele with the highest frequency, if known. Or you may choose to discard multi-allelic variants altogether from your analysis. There are other software programs you can use to re-impute multil-allelic variants after imputation of only bi-allelic variants with STITCH, for instance I imagine Beagle would handle this problem. 

Apologies but I'm not going to be able to change the code to make STITCH do the proper thing at multi (tri) allelic variants.

Thanks

Robbie

On Tue, Feb 27, 2024 at 4:30 PM Nahla Hussien AbouEl Ela <nahlaa...@gmail.com> wrote:

Using stitch, I have a triallelic snp positions, I tried to normalized to keep it, however, STITCH not accept repeated positions, how to fix it? 

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