Best way to list variants in UK Biobank bed files

Question

[davidjohngreen]

I'm working with the UK Biobank genotype call .bed files and trying to match the variants to some that I have rsIDs for (some are a bit dodgy). I'd like a simple way to list all the variants in a particular .bed file so that I can crosscheck whether the ref/alt actually match what I expect for these rsIDs, as some are a bit ambiguous. What is the best command for this in plink?

Desired output would have the REF and ALT and the GRCh37 coordinate for all variations in the .bed file.

Any advice appreciated! =)

[Pierre Lindenbaum]

nd the GRCh37 coordinate

ukbiobank is GRCh37 ?

[Pierre Lindenbaum]

o list all the variants in a particular .bed file so that

bcftools query --regions-file in.bed -f '%CHROM\t%POS0\t%END\t%ID\n'  in.vcf.gz