Error low % of SNPs used

Festus

2021-07-21

Categories: FAQ Tags: PrediXcan SPrediXcan

Possible explanation

There are different reasons where you could get a low % of SNPs in the model used with your individual level data or summary stats file. Some of the issues include;

  1. Little overlap between the model SNPs and genotype/summary stats SNPs

  2. Incomplete/malformed models .db file especially when downloading

  3. Using only a few chromosomes to run prediXcan

Possible solution

  • Perform a “manual” inspection of the data. It is recommended you use an interactive environment like R or ipython - then load the model data and GWAS data and check the intersection of variants in model and GWAS.

  • When using variant ids check if the model variant ids and the genotype/summary stats variant ids are in the same genome build. If they are not use the liftover option to generate a variant id that matches the models variant id.

    The argument for the lift over is:
    –liftover path/to/hg19ToHg38.over.chain.gz
    –on_the_fly_mapping METADATA “chr{}    {}{}{}_b38”

    On the fly mapping informs the tool how to recreate the variant name from the co ordinates to match the variant id format in the model.

Reuse

Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The source code is licensed under MIT.

Suggest changes

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Citation

For attribution, please cite this work as

Festus (2021). Error low % of SNPs used. PredictDB. /post/2021/07/21/error-low-of-snps-used/

BibTeX citation

@misc{
  title = "Error low % of SNPs used",
  author = "Festus",
  year = "2021",
  journal = "PredictDB",
  note = "/post/2021/07/21/error-low-of-snps-used/"
}