What should the genotype prefix of bgen be for regenie burden test step 2?

Former User of DNAx Community_52

Hi! I am following UKB tutorial of burden test using regenie posted on "https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/using-regenie-to-generate-variant-masks".

 

I met some issues while running regenie step 2. Step 2 in the tutorial requires a ${genotype_prefix}.bgen as input:

 

./regenie_v2.2.4.gz_x86_64_Linux_mkl \

--step 2 \

--ignore-pred \

--bgen ${genotype_prefix}.bgen \

--ref-first \

--sample ${genotype_prefix}.sample \

--phenoFile $phenotype_file \

--covarFile $phenotype_file \

--phenoCol LDL \

--covarColList Sex,Age,Age_Sq,Age_x_Sex,PC{1:10} \

--set-list "${path_to_300kwes_helper_files}/ukb23145_300k_OQFE.sets.txt.gz" \

--anno-file "${path_to_300kwes_helper_files}/ukb23145_300k_OQFE.annotations.txt.gz" \

--mask-def "${path_to_300kwes_helper_files}/ukb23145_300k_OQFE.masks" \

--aaf-bins 0.01,0.001 \

--bsize 200 \

--extract-setlist "PCSK9(ENSG00000169174)" \

--out ldl_pcsk9_test

 

I attempted with the following genotype_prefix and failed with the same error report ".bgen does not exist for option --bgen"

genotype_prefix=ukb23159_c1_b0_v1

genotype_prefix="/Bulk/Exome sequences/Population level exome OQFE variants, BGEN format - final release/ukb23159_c1_b0_v1"

genotype_prefix="/Bulk/Exome sequences/Population\ level\ exome\ OQFE\ variants,\ BGEN\ format\ -\ final\ release/ukb23159_c1_b0_v1"

genotype_prefix="/mnt/project/Bulk/Exome sequences/Population\ level\ exome\ OQFE\ variants,\ BGEN\ format\ -\ final\ release/ukb23159_c1_b0_v1"

genotype_prefix="project-id/Bulk/Exome sequences/Population\ level\ exome\ OQFE\ variants,\ BGEN\ format\ -\ final\ release/ukb23159_c1_b0_v1"

 

Does anyone know what is the correct format of the genotype_prefix to put here? Thanks!

 

Comments

1 comment

Date Votes
  • Comment author
    Chai Fungtammasan DNAnexus Team

    This is described in that doc itself (see the box above your command; I also copy and paste it here). The answer depend on which file you are analyzing.

     

    # Specify phenotype file and BGEN genotype file prefix

    phenotype_file=/path/to/phenotype_file

    genotype_prefix=/prefix/of/oqfe_bgen_file_chr

    0

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