check for duplicated IDs

UW-GAC / dbgaptools

R package to create and check standard files for dbGaP submission

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check for duplicated IDs #12

Closed smgogarten closed 5 years ago

smgogarten commented 6 years ago

Would be helpful to have a check if SAMPLE_ID and SUBJECT_ID are unique in the sample-level and subject-level files, respectively.

sarahcn commented 6 years ago

check_sattr and check_ssm identify duplicate samples; check_pheno identifies duplicate subject ID. but looks like there needs to be additional checks for (1) duplicate subject in subject consent file and possibly (2) duplicate subject in pedigree file (though i wonder if GWASTools::pedigree_check already takes care of that

smgogarten commented 5 years ago

GWASTools::pedigree_check does not check for duplicates, so do it here

smgogarten commented 5 years ago

Fixed in e3b3421