ASEReadCounter - What to use as the VCF variant reference

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Ferran Llobet Cabau

• February 14, 2024 08:08

Hi,

I am interested in doing an ASE analysis using ASEReadCounter but this tool requires a VCF refrence file. I have not been able to find any guide in what to use as this VCF file. I am not working in humans. I am worried about what to choose:

- The variants annotated in ensembl

- Imputed variant data

- Variants called of the same RNA-Seq data

I suppose the last is the worst opption since it would create a strong bias. Is it better to use annotated variants or the imputed data (which is of my population, in spite of the false genotypes)?

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  SkyWarrior

  • February 15, 2024 22:04

  Hi Ferran Llobet Cabau

  You may check the latest documentation on the tool and the reference bioarxiv paper about this tool. Looks like the 3rd one is the choice for you. 

  https://gatk.broadinstitute.org/hc/en-us/articles/21905129540507-ASEReadCounter 

  https://www.biorxiv.org/content/biorxiv/early/2015/03/05/016097.full.pdf 

  

   

  I hope this helps.

  Regards. 

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