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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
The text was updated successfully, but these errors were encountered:
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
The text was updated successfully, but these errors were encountered: