CHrX warning

[medinacarolina]

I was checking the log files after creation of the kinship matrices I noticed a warning

NOTE: In hemizygous region, males have [ 4870 ] missing genotypes and [ 4870 ] of them are due to wrong coding. Please confirm male genotypes are coded correctly, in particular, do not code them as '0/1'.

However when reading the manual from RVTEST it is written
"Prepare data. According to VCF standard, male genotype needs to coded as 0 or 1. For compatibility, rvtests also support 0/0 or 1/1 coding.
In VCF files, male genotypes can be written as "0", "1", "0|0", "0/0", "1|1", "1/1". All other genotypes will be treated as missing.

Genotype in the regression model. For consistencmaine, male genotypes are converted to 0 or 2.

I am quite confused what is going on, imputed data was download from Michigan server and is in build 37