search

Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
Apache License 2.0
437 stars 149 forks source link

Haplo results interpratation #1655

Open Jokendo-collab opened 2 months ago

Jokendo-collab commented 2 months ago

I am getting the following results with haplo analysis:

138 TL_T12:2    
12  TL_T12:2,TL_T24:1   
1   TL_T12:2,TL_T24:1,WIK_T12:2,WIK_T24:1   
6   TL_T12:2,TL_T24:2   
2   TL_T12:2,TL_T24:2,TL_T6:2   
1   TL_T12:2,TL_T6:1    
2   TL_T12:2,TU_T12:1   
2   TL_T12:2,TU_T12:2   
4   TL_T12:2,WIK_T12:1  
9   TL_T12:2,WIK_T12:2  
850 TL_T24:1

What is the difference in TL_T12:2 and TL_T24:1 how do I make sense of this? Do these numbers after the : have a significant meaning that I need to tell a story?

nuno-agostinho commented 2 months ago

Hi @Jokendo-collab,

Thank you for your interest in using Haplosaurus (haplo)!

Those results are comma-separated lists of sample:count (i.e., the count number for each sample) that exhibit the haplotype described. For more information on using and interpreting Haplosaurus, please read our public documentation.

Hope this makes it clearer, but tell me if otherwise.

Kind regards, Nuno