sex UNKNOWN

[jeffverboon]

Hi I am trying to run peddy on a vcf of ~1500 individuals genotype with the mega EX array. The ancestry analyses seem to be okay. However, I am not getting predicted sexes for some reason. The STDOUT for the sex check is:
peddy.cli[15732] INFO sex_check
warning: not all samples in PED found in VCF
peddy.peddy[15732] INFO sex-check: 1876 skipped / 23858 kept

From what I can see, the not all samples warnings just has to do with the header line of the ped.

The head of the sex.check file is:
error,het_count,het_ratio,hom_alt_count,hom_ref_count,ped_sex,predicted_sex,samp
True,0,-0.06,0,0,male,UNKNOWN,202066010233_R01C01
True,0,-0.06,0,0,female,UNKNOWN,202066010233_R02C01
True,0,-0.06,0,0,female,UNKNOWN,202066010233_R03C01
True,0,-0.06,0,0,male,UNKNOWN,202066010233_R05C01
True,0,-0.06,0,0,female,UNKNOWN,202066010233_R06C01
True,0,-0.06,0,0,female,UNKNOWN,202066010233_R07C01

[brentp]

Can you share the first 10K variants or so from chrX for one of the samples that comes up as unknown?