can't use map and ped files in plink

[ruby i]

Good morning,

I hope I am not overlooking something simple but I am trying to read my stacks output files into plink and keep getting a variety of errors. I removed the header from stacks in case that was the problem but it persists.

I also tried to bypass the stacks created plink files completely but when I made new map and ped files with vcftools and plink itself, those also failed to read in-this time due to 

Is there a common fix here that anyone is aware of?

I am attaching the text file, issues are noted near the bottom. I really hope it is just something silly I am overlooking...

I really appreciate any help or insights!

-Ruby

[Catchen, Julian]

Hi Ruby,

 

The errors I see in your file seem to all have to do with chromosome names, and PLINK expects human chromosome identifiers, from the website:

 

https://zzz.bwh.harvard.edu/plink/data.shtml#plink

By default, each line of the MAP file describes a single marker and must contain exactly 4 columns:

     chromosome (1-22, X, Y or 0 if unplaced)

     rs# or snp identifier

     Genetic distance (morgans)

     Base-pair position (bp units)

Genetic distance can be specified in centimorgans with the --cm flag. Alternatively, you can use a MAP file with the genetic distance excluded by adding the flag --map3, i.e.

plink --file mydata --map3

In this case, the three columns are expected to be

     chromosome (1-22, X, Y or 0 if unplaced)

     rs# or snp identifier

     Base-pair position (bp units)

Base-pair positions are expected to correspond to positive integers within the range of typical human chromosome sizes.

 

 

If your data are de novo, then they are unplaced and labeled “un” in the map file, you may need to replace that with “0”.  However, I think a reference genome is required for most of the functionality in PLINK (e.g. LD analysis) but I am not a PLINK expert so YMMV.

 

julian

 

 

--
Stacks website: http://catchenlab.life.illinois.edu/stacks/
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