Handing scafflold names for plink bed file

Question

[nitinra]

Hello all,

I am trying to convert vcf file to bed file using plink pipeline. I used the following command: plink --vcf input.vcf --make-bed --o output

However, I had to change the names of my chromosomes to just numbers using awk command:

awk '{gsub(/^Chromosome_/,""); print}' no_chr1.vcf > no_chr2.vcf

I also have a lot of scaffolds in the genome such as

modScaffold_4_1

How do I go about changing it in a way that plink does not throw this error and that it does not overlap with already present chromosome numbers:

Invalid chromosome code '4_1' on line 13386275 of .vcf file.

My final step is to convert it to a bed file and use it in admixture software.

[Pierre Lindenbaum]

did you try to use the option --allow-extra-chr ?

[nitinra]

I did and the analysis runs. however, It shows up as an error when I use it in admixture since the names are still present for scaffolds.

[rs146]

Hi, I am currently having the same issue. Have you managed to solve this?

[dobata]

I was finally successful by setting --allow-extra-chr 0. This seems to convert all scaffold names into 0, but indeed it works.