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Using Peas To Convert Hapmap To Plink Format

hello, everyone!

i am using the peas software for file format conversion test. The data i used is the data peas offered. I use 1.1HapMapDatatoStandard part first convert the hapmap data to standard mode, and then changed the suffix to inp while modify pops.inp for calculation.

when i get the ped and map(pedsnp original file) files, i use the plink software cmds:

plink --file 1pops(file name for ped and map) --r2 --noweb for LD calculation, but it turns out to be wrong: 

plink --file 1pops --r2 --noweb

@----------------------------------------------------------@
|        PLINK!       |     v1.07      |   10/Aug/2009     |
|----------------------------------------------------------|
|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Skipping web check... [ --noweb ]
Writing this text to log file [ plink.log ]
Analysis started: Tue May 31 21:10:52 2011

Options in effect:
        --file 1pops
        --r2
        --noweb

54881 (of 54881) markers to be included from [ 1pops.map ]

ERROR:
A problem with line 1 in [ 1pops.ped ]
Expecting 6 + 2 * 54881 = 109768 columns, but found 106612

i tried several times and checked the file, but i have not seen any problem yet. So could anybody here tell me which part goes wrong?

and why do the plink software need the formula to check the columns?

plink linkage
• 4,922 views • link
updated by User 0422 • User 0422 • written by J.F.Jiang J.F.Jiang

I'm closing this question. As far as I can see in the last comment, the problem has been solved.

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

Hi,

There seems some problem in your ped file as from your example it seems like you have 54881 markers which should give 54881x2 (as it is diploid loci)= 109762 columns of data plus 6 columns more for plink formats which includes following 6 columns about sample.

Family ID Individual ID Paternal ID Maternal ID Sex (1=male; 2=female; other=unknown) Phenotype

It seems to me that peas didn't convert your input file properly!

regards,

Bio

• 0 views • link
written by User 0422 • User 0422

yes,i have contact the original author of peas, and the designer kindly offer me great suggestion about the software, and after our discussion, the software had been greatly improved and now can be easily used for my file format conversion.

• 0 views • link
written by J.F.Jiang J.F.Jiang

Hi I am facing the same problem. How could you overcome the problem? please give me the suggestion.

• 1 views • link
written by iamsudipta.rocker • iamsudipta.rocker

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