GCTA make GRM error contains illegal chr number

Question

[Emy]

Hi

I created bim, fam, and bed files by Plink with the use of these codes.

> shell("plink --file r --maf 0.05 --geno 0.01 --mind 0.1 --hwe 1e-6
> --nonfounders --horse --make-bed --out r") 
> 
> shell("plink --file r --maf 0.05 --geno 0.01 --mind 0.1 --hwe 1e-6
> --nonfounders --horse --recode --out r") 
> 
> 
> shell("plink --file r --maf 0.05 --geno 0.01 --mind 0.1 --hwe 1e-6
> --nonfounders --horse --recodeA --out rA") 
> 
> shell("plink --file r --maf 0.05 --geno 0.01 --mind 0.1 --hwe 1e-6
> --nonfounders --horse --recodeAD --out rAD")

Now, I want to create GRM by GCTA software.

> gcta64  --bfile r  --autosome  --make-grm  --out r

But I am faced with an error.

Error: Line 1015 of [file.bim] contains illegal chr number, please check
Line of 1015:   27  M2609   0   913820  1   2

I removed this line but I see again this error in another line.

How can I solve this problem?

Thank you for your time

[zx8754]

Maybe find all the rows with "illegal chr number" and fix them.

Answer 1

[Lemire]

By default GCTA assumes human genome (22 pairs of autosomal chromosomes). For your horse genome, set the autosome-num flag to the appropriate number.

From https://cnsgenomics.com/software/gcta/#Datamanagement :

--autosome-num 22
Specify the number of autosomes for a species other than human. For example, if you specify the number of autosomes to be 19, then chromosomes 1 to 19 will be recognized as autosomes and chromosome 20 will be recognized as the X chromosome. The default number is 22 if this option not specified.

Answer 2

[Emy]

Thank you for your help. I did that.

I put --autosome-num 29 for making GRM and MLMA.