"--oxford-single-chr" option for .bgen file format?

[Andrew Jaffe]

Hi, I can't seem to get the --oxford-single-chr option to work with the .bgen file format:

plink --bgen GEN_files/tmp_chr$chr.bgen --sample GEN_files/tmp.sample --make-bed --out imputed_plinkFiles/chr$chr.imputed --oxford-single-chr $chr 

PLINK v1.90b3a 64-bit (12 Jan 2015)        https://www.cog-genomics.org/plink2

(C) 2005-2015 Shaun Purcell, Christopher Chang   GNU General Public License v3

Logging to imputed_plinkFiles/chr21.imputed.log.

Error: --oxford-single-chr must be used with .gen input.

For more information, try 'plink --help [flag name]' or 'plink --help | more'.

Thanks,

Andrew

[Christopher Chang]

This isn't currently implemented, but I can add it if it's necessary.  Can you send me a small .bgen file which requires this option to be converted properly, so I can check how it's formatted?

[Andrew Jaffe]

This has a description of the file format, http://www.well.ox.ac.uk/~gav/bgen_format/bgen_format.html

I've attached a .bgen file and corresponding .gen file (plus sample file) for ~1000 samples for the first 10 SNPs on chr21

Subsequently, instead of adding functionality, you could instead just clarify the error message, since I think .bgen is considered Oxford formatted as well (I think its analogous to plink: ped/map --> bim/bed/fam) 

'Error: --oxford-single-chr must be used with .gen or gen.gz input (not .bgen).'

Thanks,

A

[Christopher Chang]

This .bgen is already converted correctly by PLINK.  No alternate single-chromosome mode is needed.

I will clarify the error message.