search

brentp / peddy

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF
MIT License
133 stars 39 forks source link

sex UNKNOWN #43

Open jeffverboon opened 6 years ago

jeffverboon commented 6 years ago

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 commented 6 years ago

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