PLINK 1.9 update-chr || log says variants updated by bim file doesn't reflect

[sanjee...@gmail.com]

Hi Chris,

Hope you're doing well.

I am using: PLINK v1.90b4.9 64-bit (13 Oct 2017)

I would like to update CHR of SNPs in the plink file.

I use following command

 plink --bfile MHAS--update-chr update_chr.txt --make-bed --out MHAS_updatedCHR

First few lines (tab separated) of update_chr.txt are

 head update_chr.txt

1:13130264      chr1

rs116587930     chr1

rs3131972       chr1

rs114525117     chr1

rs12127425      chr1

rs28678693      chr1

rs4970382       chr1

The CHR are not updated. I am wondering why.

Output  after running the above commands are :

head MHAS_updatedCHR.bim

1       1:13130264      0       8335    G       A

1       rs116587930     0       792461  A       G

1       rs3131972       0       817341  A       G

1       rs114525117     0       823656  A       G

The attached log says that that --update-chr: 413228 values updated

But they are not reflected into the output file.

Can you please help?

Thank you

[Christopher Chang]

Because "1" and "chr1" are both very common, plink automatically treats them as the same thing.  Use the --output-chr flag, not --update-chr, to control whether the "1" or "chr1" encoding is used in plink output files.

[sanjee...@gmail.com]

I was able to fix this using

 --output-chr chrM

Thank you