Plink --merge-list only outputting fam
Entering edit mode
5 weeks ago
J • 0

I am attempting to merge Plink files towards an algorithm I am using (CookHLA). I have already made the bed/bim/fam files for my vcf files. Now, I want to merge them into a single file so I can progress with the algorithm.

To do this, I am running the following line of code:

plink --bfile 0002 --merge-list PLINK_UniqueNames --make-bed --threads 4 --out Merged_Plink_files

0002 refers to the first set of plink out (I am unsure what to use as a reference). I am getting lots of warnings about non ATGC variants, ie '.'.

My issue is that only a fam file is outputted when I need the full set. I was hoping for some assistance. I admittedly do not have much experience with Plink so any assistance would be appreciated.

Contents of the fam file (just a few lines):

0002    0002    0   0   0   -9
0005    0005    0   0   0   -9
0007    0007    0   0   0   -9
0008    0008    0   0   0   -9
0009    0009    0   0   0   -9
001 001 0   0   0   -9
plink bash • 312 views
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What is PLINK_UniqueNames ? --merge-list requires a file, every row in that file refers to separate plink file:

--merge-list <filename>

This allows you to merge more than one fileset to the reference fileset. (Also, this can be used without a reference; in that case, the newly created fileset is then treated as the reference by most other PLINK operations.) The parameter must be the name of a text file specifying one fileset per line.

  • If a line contains only one name, it is assumed to be the prefix for a binary fileset.
  • If a line contains exactly two names, they are assumed to be the full filenames for a text fileset (.ped, then .map). These filesets may not contain multi-character alleles.
  • If a line contains exactly three names, they are assumed to be the full filenames for a binary fileset (.bed, then .bim, then .fam).

Alternatively, you can use bcftools to merge all vcfs into one, then use plink to read that one merged vcf.

Entering edit mode

That is a file that contains the prefix to all the files

Entering edit mode

Rather than further pursuing this path, I am taking a step back and merging the VCF files and then using plink, which I did not consider before. This removes the need to work with extra processing steps.

Entering edit mode
4 weeks ago

If plink is only generating a .fam, that implies that an error occurred. Yet you did not post a .log containing the error message, or describing what happened at all.


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