Plink: LD-clumping of .dosage/.fam files

Question

[hessjl]

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!

Answer 1

[chrchang523]

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

[hessjl]

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 :(

[chrchang523]

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.

[hessjl]

Thanks for bringing clarity to this!