How to deal with qctool Error: sample file and genotype file sample IDs do not match!
Trying to convert BGEN files from zstd to zlib, using code from UKB_RAP/format_conversion/bgen_compression_conversion.md at main · dnanexus/UKB_RAP · GitHub
But occurred this:
Welcome to qctool
(version: 2.2.0, revision: unknown)
(C) 2009-2020 University of Oxford
Opening genotype files : [ ] (0/22,0.0s,0.0/s)
Opening genotype files : [* ] (1/22,1.3s,0.8/s)
Opening genotype files : [**** ] (3/22,2.3s,1.3/s)
Opening genotype files : [******** ] (6/22,3.7s,1.6/s)
Opening genotype files : [******************************] (22/22,2.3s,9.4/s)
Opening genotype files : [******************************] (22/22,2.3s,9.4/s)
!! Error: sample file and genotype file sample IDs do not match!
!! First mismatch is at sample 1: IDs are "XYZ" and "YXZ".
terminate called after throwing an instance of 'genfile::MismatchError'
what(): genfile::MismatchError
Comments
2 comments
Which field id and data type you work with? Are you working with 21008 "Imputation from genotype (Genomics England)"?
Possible issues with the sample files in GEL and TOPMed Impute datasets have been discussed in the following threads:
https://community.dnanexus.com/s/question/0D5t000004SBxtyCAD/potential-issues-with-imputed-data
https://community.dnanexus.com/s/question/0D5t000004CaydsCAB/have-questions-about-the-gel-or-topmed-impute-data-release-ask-them-here
If the issue persists, let Community know and it would be also better to redirect this question to UKB-RAP Support team, as they will be able to access your project and inspect the issue in detail.
ukbiobank-support@dnanexus.com
Thank you! I apologize for bringing up the same question again.
I managed to resolve the error with qctool by not including the 'sample' parameter.
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