Plink --merge-list generating error

Question

[MAPK]

I am running plink --merge-list to merge plink files, but not sure why I am getting this error below. Can someone please help me troubleshoot this? Thanks!

[aneu@HPC test]$ cat mylist.list

chr12.bed
chr12.bim
chr12.fam
chr13.bed
chr13.bim
chr13.fam
chr14.bed
chr14.bim
chr14.fam

[aneu@HPC test]$ ls

chr12.bed chr12.bim  chr12.fam  chr13.bed chr13.bim chr13.fam  chr14.bed  chr14.bim chr14.fam mylist.list

[aneu@HPC]$ plink1.9 --bfile --merge-list mylist.list --make-bed --out merged

PLINK v1.90b6.4 64-bit (7 Aug 2018)            www.cog-genomics.org/plink/1.9/
(C) 2005-2018 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to merged.log.
Options in effect:
  --bfile
  --make-bed
  --memory 100000
  --merge-list mylist.list
  --out merged
  --threads 12

773748 MB RAM detected; reserving 100000 MB for main workspace.
Error: Failed to open plink.bed.
[aneu@ test]$

Answer 1

[Sam]

You need to provide a reference file with the --bfile field.

Using your example, you will have a merge list of

chr13
chr14

then you can do

./plink \
  --bfile chr12 \
  --make-bed \
  --memory 100000 \
  --merge-list mylist.list \
  --out merged \
  --threads 12

[MAPK]

Thanks, that actually worked. I don't know why they had this on their instructions.

--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.)

[Sam]

I guess that's because you included --bfile in your original command