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