bgen and qctool
Giulia Pontali
Hi,
I need to prepare a .bgen file to use with qctool. I’m currently running the following command:
plink2 --pfile chr22 --export bgen-1.2 bits=8 id-paste=fid,iid id-delim=: --out mydata
However, when I run qctool, I get the following error:
qctool -g mydata.bgen -snp-stats -osnp out
!! Error (genfile::BadArgumentError): In argument(s) order_type=6, value_type=1 to function genfile::ToGP::set_number_of_entries(): Unsupported order_type/value_type combination..
Would you like me to also help explain or fix the actual error (Unsupported order_type/value_type combination)?
It’s likely due to how plink2 exports the BGEN format (especially with bits=8) and qctool not supporting that combination.
than you,
Giulia
Chris Chang
--
You received this message because you are subscribed to the Google Groups "plink2-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to plink2-users...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/plink2-users/83407a75-2d0f-49c4-968c-43f2469bf1c6n%40googlegroups.com.
Giulia Pontali
Welcome to qctool
(version: 2.2.0, revision: unknown)
(C) 2009-2020 University of Oxford
Opening genotype files : [******************************] (1/1,0.0s,23.4/s)
========================================================================
Input SAMPLE file(s): Output SAMPLE file: "(n/a)".
Sample exclusion output file: "(n/a)".
Input GEN file(s):
( 219305 snps) "mydata.bgen (bgen v1.2; 9219 named samples; zlib compression)"
(total 219305 snps in 1 sources).
Number of samples: 9219
Output GEN file(s): (n/a)
Output SNP position file(s): (n/a)
Sample filter: .
# of samples in input files: 9219.
# of samples after filtering: 9219 (0 filtered out).
========================================================================
SNPSummaryComponent: the following components are in place:
HWEComputation
AlleleFrequencyComputation
InfoComputation
MissingnessComputation
Processing SNPs : (0/?,0.1s,0.0/s)
========================================================================
Number of SNPs:
-- in input file(s): 219305.
-- in output file(s): 0
Number of samples in input file(s): 9219.
========================================================================
!! Error (genfile::BadArgumentError): In argument(s) order_type=6, value_type=1 to function genfile::ToGP::set_number_of_entries(): Unsupported order_type/value_type combination..
Thank you for using qctool.
Chris Chang
Giulia Pontali
PLINK v2.00a6LM AVX2 Intel (26 May 2024)
Options in effect:
--export bgen-1.2 bits=8 id-paste=fid,iid id-delim=:
--out mydata
--pfile chr22
Hostname: hnode02
Working directory: /scratch/giulia.pontali/belive_qctool
Start time: Mon Nov 3 16:49:27 2025
Random number seed: 1762184967
384915 MiB RAM detected, ~353068 available; reserving 192457 MiB for main
workspace.
Using up to 40 threads (change this with --threads).
9219 samples (0 females, 0 males, 9219 ambiguous; 9219 founders) loaded from
chr22.psam.
219305 variants loaded from chr22.pvar.
Note: No phenotype data present.
Warning: Unphased heterozygous hardcalls in partially-phased variants are
poorly represented with bits=8.
It is necessary to use e.g. --dosage-erase-threshold 0.006 to re-import them
cleanly.
Writing mydata.bgen ... done.
Writing mydata.sample ... done.
End time: Mon Nov 3 16:49:32 2025