Question: Conditional analysis on dosage file -what program to use?
0
gravatar for Mamta
3.4 years ago by
Mamta460
United States
Mamta460 wrote:

HI all,

i have recived some files that I fail to understand the header as the dosage info is ok with 3 probabilities for each sample.

This was used for the association analysis in plink list skip0=0 skip1=0 format=3 case-control-freqs

PLINK v1.90b3.43 64-bit (13 Nov 2016) Options in effect: --allow-no-sex --covar file.covar --covar-number 4 --dosage file.gprobs.list list skip0=0 skip1=0 format=3 case-control-freqs --fam file.fam --out result.assoc --pheno file.pheno

However, I cannot do conditional analysis on this. So was hoping to convert them to ped to do conditional. Can someone help me how to convert and/or understand the file format to make ped file.

Thanks so much!!!

ADD COMMENTlink modified 3.2 years ago by pfs280 • written 3.4 years ago by Mamta460
1
gravatar for pfs
3.2 years ago by
pfs280
USA/Boston
pfs280 wrote:

I would install plink2 and then run the command - plink2 --gen '..gen', --missing-code 'what missing values are encoded as in your .sample file' --sample '..sample' --oxford-single-chr 'chr_num' . This should get you started.

ADD COMMENTlink written 3.2 years ago by pfs280
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 970 users visited in the last hour
_