Question: Plink: LD-clumping of .dosage/.fam files
1
gravatar for hessjl
3.8 years ago by
hessjl50
United States
hessjl50 wrote:

 

Here's a breakdown of my situation. I'm trying to pass to pass the following command options in Plink:


--dosage MY_DATA.dosage
--fam MY_DATA.fam
--clump GWASresults.assoc
--clump-p1 1
--clump-p2 1 
--clump-r2 0.1
--clump-kb 500
--out MY_DATA_CLUMPED


Strangely, this returns an association summary file. It's as though Plink is ignoring these prompts to clump, and proceeds with a default track of testing for allele association to the phenotype. I expected this to turnover a file type similar to that presented in an example from the Plink website: 

 CHR  F         SNP         BP         P  TOTAL   NSIG    S05    S01   S001  S0001    SP2
      8  1   rs1234564   15716326  5.01e-07      0      0      0      0      0      0   NONE
     14  1   rs1205236   69831825  1.46e-06      0      0      0      0      0      0   NONE
      2  1  rs16331058  114547107  2.33e-06      3      0      0      0      0      3   rs2366902(1),...
      2  1    rs759966   54902416  9.28e-06      4      0      0      0      3      1   rs12538389(1),...
     11  1   rs8031586   44633498  9.75e-06      1      0      0      0      0      1   rs802328(1)
     12  1  rs12431413   30028246  9.89e-06      0      0      0      0      0      0   NONE
      6  1  rs14966070   62091121  1.07e-05      0      0      0      0      0      0   NONE

 

For reference, MY_DATA (--dosage file) is formatted as shown in this example:

SNP  A1  A2   F1 I1       F2 I2        F3 I3
     rs0001   A   C   0.98 0.02   1.00 0.00    0.00 0.01 
     rs0002   G   A   0.00 1.00   0.00 0.00    0.99 0.01 

 

Has anyone successfully "clumped" dosage data? If so, what commands should I be passing to get the expected output?

Thanks for considering my question! 

 

 

 

 

 

clump r2 plink dosage linkage • 1.8k views
ADD COMMENTlink modified 3.8 years ago by chrchang5234.8k • written 3.8 years ago by hessjl50
1
gravatar for chrchang523
3.8 years ago by
chrchang5234.8k
United States
chrchang5234.8k wrote:

PLINK's LD computations do not currently work on .dosage files.

ADD COMMENTlink written 3.8 years ago by chrchang5234.8k

Bummer! And do you know off hand of a program that converts the style of .dosage files I'm working with to say .ped? The --make-bed option doesn't produce anything valid :(

 

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by hessjl50

I'm not aware of one, though it shouldn't be too difficult to write a script for this.  PLINK 1.9 is only capable of performing this conversion for Oxford .gen files.

ADD REPLYlink written 3.8 years ago by chrchang5234.8k

Thanks for bringing clarity to this! 

ADD REPLYlink written 3.8 years ago by hessjl50
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