AFpredictoR

Sometimes sumstats report allele frequency (AF) information but is not clear which allele the AF belongs to. AFpredictoR predicts which allele the AF belongs to and outputs a new summary statistics file.

The name can be a bit misleading as it predicts and assigns the AF to the appropriate allele rather than predicting the AF value itself.
Please recommend a new name if you have one :).

Required packages

• data.table
• VarianceGamma

How to run

./AFpredictoR.R \
    /path/to/sumstats.txt \
    /path/to/cohort.bim \
    /path/to/cohort.frqx.gz \
    predicted-sumstats

sumstats.txt

The data.table::fread function is used to read the data.
Assumes that the sumstats has the following columns:

• SNP: Variant ID in the summary statistics file
• chrom: Chromosome position of the variant
• pos: Basepair position of the variant on the chromosome
• A1: Usually the effect allele.
• A2: Usually the other allele
• AF: Allele frequency for the unknown allele (A1 or A2)
• N: Sample size of the variant

cohort.bim

The .bim file from the Plink binary genotype dataset (See link).

cohort.frqx.gz

The .frqx.gz file created using Plink's --freqx gz command (See link)

/path/to/<prefix>

The output prefix. <prefix>.csv and <prefix>.debug.csv file will be generated.

Output

<prefix>.tsv

Same format as the input summary statistics file, except that the AF column now refers to the frequency for A1