Allele frequency column does not match N_REF,N_HET,N_ALT column

[sgrosche]

Dear Xiaowei, thank you for developing rvtests. I am using your tool and have realized that from version 20160504 on the allele frequencies reported and the INFORMATIVE_ALT_AC column do not match the numbers reported in the N_REF,N_HET and N_ALT columns if the dosage tag (--dosage) is used. Also the results in the allele frequency column, the INFORMATIVE_ALT_AC column and the ALT_EFFSIZE column differ between version 20151007 and newer versions when using the --dosage tag and the same input file. The N_REF,N_HET and N_ALT columns, pvalues and the U_STAT,SQRT_V_STAT columns remain the same between versions. Could you tell me where the differences occur from? Thank you very much and best wishes, Sarah

[zhanxw]

It is most likely that dosages are not integers, and there are rounding errors. For example, if the dosage is 1.5, and the genotype is 1, you will get allele counts of 2 and 1 respectively.