pseudochromosomes in VCFtools

Question

[truebeliever24]

Hi everybody,

I am trying to study individual chromosomes in my dataset, and create a plink file in vcftools with a single chromosome. However the chromosomes are labeled as Pseudochromosome_1, 2, 3, etc. Thus, when I enter the command:

vcftools --vcf filename.vcf --plink --chr 1 --out filename

I don't know what to enter for "chr" - 1, 2, 3, etc does not work.

Thanks for your help!

Answer 1

[chrchang523]

vcftools is mostly obsolete. plink 1.9 and 2.0 can directly import VCFs, and they do it far more efficiently than vcftools can "export to plink". (Use plink's --allow-extra-chr flag to permit chromosome codes like "Pseudochromosome_1".) bcftools contains better implementations of most of vcftools's other functions.

[truebeliever24]

Thank you! This helped a lot. Now, my dataset is only showing "Pseudochromosome_1" and "Pseudochromosome_2"...when I have 33 chromosomes in my dataset. How can I convert all 33 chromosomes instead of Pseudo 1 and 2?