I've been attempting to write a script to run on DNA Nexus to identify variants in the UK Biobank imputed data based on rsid and export them as a plink binary file for further analysis
The command
zcat /mnt/project/Bulk/Imputation/Imputation\ from\ genotype\ (TOPmed)/helper_files/ukb21007_c1_b0_v1.sites.vcf.gz | grep 'rs138638958'
pulls one line out of the helper file, implying that this SNP is in the data
However, the command
bgenix -g "/mnt/project/Bulk/Imputation/Imputation from genotype (TOPmed)/ukb21007_c1_b0_v1.bgen" -incl-rsids rs138638958
tells me bgenix wrote data for 0 variants to stdout
Why is it in the helper file but bgenix can't find it in the associated bgen file?
I've been using bgenix from the link https://www.chg.ox.ac.uk/~gav/resources/bgen_v1.1.4-Ubuntu16.04-x86_64.tgz
