sereeena

Can anyone confirm? I believe this is a bug in the driver, where documents can't be returned from Database.Query if the AQL query is returning a document or projection from...

Great, adding this flag does let DosageConvertor read the file now! I have another problem though, the dosage file that minimac4 produces now (with that flag -f DS) does not...

Yes of course. Previously, the dosage file produced from minimac 1.0.3: ``` head -n 20 23andme_chr5_minimac4.dose.vcf ##fileformat=VCFv4.1 ##filedate=2022.10.21 ##source=Minimac4.v1.0.3 ... ##FORMAT= ##FORMAT= ##minimac4_Command=minimac4 --cpus 2 --refHaps chr5.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz --haps 23andme_chr5_eagle.vcf.gz --minRatio...

Thanks for responding so quickly - I can confirm the changes you made to DosageConvertor work and I am able to create valid plink files, so creating a pull request...

Yes I agree it seems unlikely, but I've put together some files here for you to reproduce it, using the same input file and references. My pipeline runs on Centos7,...

The .msav reference files are not text files, so I'm unable to check whether the .m3vcf.gz reference files are converted correctly?

Thanks for helping with this! So it looks like there was always something wrong with our pipeline and that minimac 1.0.3 may have taken the alleles from the references while...

go get started working and I was able to get v0.4.0, but the MergeRaw function is not available in the API for this version? The Merge function used to take...

Thank you @lpic10 that's what I needed, except I am getting the 404 timeout again during go get. I guess I will wait or keep trying. Note @hhrutter your workaround...

Thank you, that seems to be solving the timeout issue!