How to resolve REGENIE errors with GEL and TOPmed BGEN indices
Sometimes the bgen .bgi files for GEL and TOPmed imputed data might cause an error with REGENIE.
For example, this is the error seen from REGENIE with the incorrect index file:
Association testing mode with fast multithreading using OpenMP
* bgen : [ukb21008_c21_b0_v1.bgen]
-summary : bgen file (v1.2 layout, zstd compressed) with 488315 anonymous samples and 4376829 variants with 8-bit encoding.
-index bgi file [ukb21008_c21_b0_v1.bgen.bgi]
ERROR: BGenError
To fix this, please try the following steps:
If you are using REGENIE in swiss-army-knife, or build your own applet, the simplest workaround is to run REGENIE without the .bgi index files, since this is an optional input.
For the REGENIE app built by DNAnexus, the .bgi index input is required. You would need to create new .bgi files using the swiss-army-knife app through the RAP.
Start the swiss-army-knife app, then provide all the .bgen files in /Bulk/Imputation/Imputation from genotype (GEL)/
or /Bulk/Imputation/Imputation from genotype (TOPmed)/
as inputs. You can filter for just the .bgen files using the Name filter, with value as /bgen$/
. Then, click on the check box at the top to select all files.

In the Command line input of swiss-army-knife, please provide the command as below:
for i in $(ls *.bgen); do bgenix -index -g ${i}; done
Then select an output folder for the new index files. Also, please select the instance type as: mem3_ssd3_x4. This will make sure that the instance has enough disk space to store all the .bgen files. The job should take around 2 hours and cost around £0.4.
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