Are writekey and onlykeyed output options implemented?

[sergiogonmoll]

Hi,

I tried running AlphaImpute2 with the following code:
AlphaImpute2 -genotypes data/Genotypes_all.txt
-pedigree data/ped_certain.txt
-out outputs/ai2_SW_geno -writekey genotypes -onlykeyed
-cycles 10 -maxthreads 12

I was hoping to get back only the imputation for those individuals that we have sequenced and we know their positions in the PLINK file we're using, but the -writekey and -onlykeyed flags are ignored and the run outputs all the individuals it can find in the pedigree and dummy individuals in alphanumeric order, instead of the order in the genotype file. I was looking at the AlphaImpute2 script and I noticed that these flags are never invoked. Is this feature not implemented as it says in the manual? I appreciate any information.

Kind regards,

Sergio

[gregorgorjanc]

@sergiogonmoll thanks for opening this issue. Indeed, the main developers rushed the public push to GitHub ahead of their departure from Roslin. Hence, some parts of the suite are not well tested. Could you create a minimal reproducible example so that we can look into the issue - it should not be too hard to fix this and we would be happy to work with you on this;)