Hello,
I am trying to update rsids then chromosome # in a PLINK file
.bim file starts out looking like this:
23 23:2700157:G:A 0 2700157 A G
23 23:2700163:G:A 0 2700163 A G
23 23:2703633:A:G 0 2703633 G A
I make a update_rsid.txt file:
23:2700157:G:A X:2700157:G:A
23:2700163:G:A X:2700163:G:A
23:2703633:A:G X:2703633:A:G
run:
plink \
--bfile my_file \
--keep-allele-order \
--update-name update_rsid.txt \
--make-bed \
--out my_file_rsid_updated
updated bim file looks good now:
23 X:2700157:G:A 0 2700157 A G
23 X:2700163:G:A 0 2700163 A G
23 X:2703633:A:G 0 2703633 G A
I make update_chr.txt:
X:2700157:G:A X
X:2700163:G:A X
X:2703633:A:G X
then try to update chrs:
plink \
--bfile my_file_rsid_updated \
--keep-allele-order \
--update-chr update_chr.txt \
--make-bed \
--out my_file_chr_updated
plink spits out this:
--update-chr: 10728 values updated.
but if I open the bim file it looks like nothing happened:
23 X:2700157:G:A 0 2700157 A G
23 X:2700163:G:A 0 2700163 A G
23 X:2703633:A:G 0 2703633 G A
Am I implementing something wrong?
plink 1.9 treats the chromosome codes “23” and “X” as interchangeable, but for backward compatibility it defaults to outputting the numeric form. Use —output-chr (https://www.cog-genomics.org/plink/1.9/data#irreg_output ) to change this for a specific run.
Note that plink 2.0 outputs X instead of 23 by default; if you don’t want to use —output-chr all the time, an alternative is to use 2.0 when possible.
when I use --output-chr X, I get error. When I use --output-chr M it seems to accurately recode my chr 23 variants as X
X X:2700157:G:A 0 2700157 A G
X X:2700163:G:A 0 2700163 A G
X X:2703633:A:G 0 2703633 G A
Does this seem right, but I am a little baffled by it so am afraid to trust without understanding. Thank you so much
As explained in the documentation, —output-chr’s argument is the mitochondrial code, since that changes the most between datasets.
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