zhanxw
commented
4 years ago This line [INFO] Loaded 0 cases, 0 controls, and 2504 missing phenotypes shows that RVTESTS cannot find the phenotype. Can you provide the first few lines of /Users/nemanjavucic/Downloads/integrated_call_samples_v2.20130502.ALL.corr.ped ?
Hello, I am using 1000 Genomes files downloaded from here to perform single variant tests. Using the chr20 VCF.GZ file and appropriate PED file the rvtests exits with the following message displayed on the stdout:
[INFO] Program version: 20190205 [INFO] Git Version: c86e589efef15382603300dc7f4c3394c82d69b8 [INFO] Parameters BEGIN ParameterList created by unknown_user on 9b3d3ec177d0 at Wed Apr 17 13:06:44 2019 --inVcf "/Users/nemanjavucic/Downloads/ALL.chr20.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf" --out "sample_test" --pheno "/Users/nemanjavucic/Downloads/integrated_call_samples_v2.20130502.ALL.corr.ped" --mpheno "1" --single "score,wald" [INFO] Parameters END [INFO] Analysis started at: Wed Apr 17 13:06:44 2019 [INFO] Loaded [ 2504 ] samples from genotype files [WARN] Skip: Missing or invalid phenotype type, skipping line 1 [ Family_ID Individual_ID Paternal_ID Maternal_ID Gender Phenotype Population Relationship Siblings Second_Order Third_Order Children Other_Comments phase_3_genotypes related_genotypes omni_genotypes affy_genotypes ] ... [INFO] Loaded [ 3691 ] sample phenotypes [INFO] Discard [ 1187 ] samples as they do not have genotypes [INFO] Loaded 1233 male, 1271 female and 0 sex-unknown samples from /Users/nemanjavucic/Downloads/integrated_call_samples_v2.20130502.ALL.corr.ped [INFO] Loaded 0 cases, 0 controls, and 2504 missing phenotypes [WARN] There are no case! [WARN] There are no control! [WARN] -- Enabling binary phenotype mode -- [FATAL] There are 0 samples with valid phenotypes, quitting...
I get similar output when selecting different columns from the PED file. Could you explain how to adopt 1000 genomes phenotype data for rvtests? Many thanks, Nemanja