• Mismatch between the model SNP ids and geneotype/gwas SNP ids, e.g using model rsids to match with genotype variant_ids

  • When having different genome builds use chr{}{}{}_{}_b38" for the –on_the_fly_mapping argument. This parameter specifies a format string to be used when building a variant id from its (liftover coordinates) and alleles (genotype). Then these ids will be matched to the ids in the mashr/elastic net model which are all hg38-based.

  • You can use a text variant mapping instead of on_the_fly_mapping as below

    The argument you would need to use is: -variant_mapping /path/to/tab-separated-file.txt KEYNAME VALUENAME where:

    a) path refers to a simple tabular file

    b) KEYNAME is the name of the column with your input variants

    c) VALUENAME is the name of the column with the mapped variant as existing in a model (NA would cause the model to be ignored)

  • When you are using mashr models they don’t use RSIDs so you need to let S-PrediXcan knows this is the case with the additional command line arguments:

    -keep_non_rsid —additional_output –model_db_snp_key varID


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For attribution, please cite this work as

Festus (2021). Error: 0 % SNPs used. ImLab Notes. /post/2021/07/20/error-0-snps-used/

BibTeX citation

  title = "Error: 0 % SNPs used",
  author = "Festus",
  year = "2021",
  journal = "ImLab Notes",
  note = "/post/2021/07/20/error-0-snps-used/"