can't get dosage to work on plink2

[Jonas Ghouse]

Anyone who can help me get this to work?

I am working on imputed GWAS chip data. 

I have performed the following QC on chromosome 22:

1) -- mind 0.10 -- geno 0.05

2) removed cryptic related individuals 

3) removed individuals with excess homo/heterozygosity >4 SD from F = 0

4) removed SNPs with a imputationsscore R2<0.3

Now, I would like to perform the association test. My variable the continuous ECG variable "QT interval". I have co-variates called "SEX", "AGE", "RR-interval" and component C1 on my MDS. 

Can't get the --dosage flag to work. 

I have tried the following (unadjusted) model as well:

plink2 --pgen dataImp/chr22_clean5.pgen \

  --psam dataImp/chr22_clean5.psam\

  --pvar dataImp/chr22_clean5.pvar\

  --keep-autoconv \

  --pheno data/qt.ped \

  --pheno-name DISEASE\

  --glm  \

  --out dataImp/chr22_assoc_undadj

Any solutions?

Sincerily

Jonas

[Jonas Ghouse]

Warning: No output requested.  (Did you forget --make-bed/--make-{b}pgen?)

Exiting.

  plink2 [input flag(s)...] {command flag(s)...} {other flag(s)...}

  plink2 --help {flag name(s)...}

Commands include --make-bpgen, --export, --freq, --geno-counts, --missing,

--hardy, --indep-pairwise, --make-king, --king-cutoff, --write-snplist,

--make-grm-gz, --pca, --glm, --genotyping-rate, --validate, and

--zst-decompress.

'plink2 --help | more' describes all functions.

vls732@porus01:/emc/cbmr/san7/fng514/lucamp_gvcf/data/jonasDir>   --linear \

>   --make-pgen \

>   --out dataImp/chr22_assoc_undadj

If '--linear' is not a typo you can use command-not-found to lookup the package that contains it, like this:

    cnf --linear

[Christopher Chang]

The --dosage flag is not implemented yet in plink 2.0; just .gen/.bgen import for now.  Also, --glm doesn't handle quantitative traits yet (though that'll be finished within 1-2 weeks).

Apologies for the incompleteness of this alpha build; the first priority has been enabling things which cannot be done at all with v1.9, like Firth regression.

[Siying Huang]

Hi Chris,

I have the same question. But I need a bit clarification for the .gen/.bgen option.  I prepared my data using PLINK 1.9 from the command of  --write-dosage, which gave me the updated data plink.out.dosage . I now want to run PCA on this file in PLINK2. Does it mean that I will have to transform the file plink.out.dosage into plink.gen format? If so is there any way to do this in any of the PLINK version?

I'd really appreciate your help on this! Thank you!

[Christopher Chang]

Not yet, but dosage import from both VCF and --write-dosage output is the next thing I'm working on; I'll post here again when it's ready.

[Christopher Chang]

--import-dosage is implemented in the May 7 build (for now, use "plink2 --help import-dosage" to see documentation; I will try to update the online documentation tomorrow night).  VCF dosage import/export is also working (e.g. "plink2 --vcf mydata.vcf dosage=DS").

On Wednesday, April 26, 2017 at 6:31:20 AM UTC-7, Siying Huang wrote: