Question: pseudochromosomes in VCFtools
gravatar for truebeliever24
19 months ago by
truebeliever2420 wrote:

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!

genome • 359 views
ADD COMMENTlink modified 19 months ago by chrchang5237.3k • written 19 months ago by truebeliever2420
gravatar for chrchang523
19 months ago by
United States
chrchang5237.3k wrote:

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.

ADD COMMENTlink written 19 months ago by chrchang5237.3k

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?

ADD REPLYlink written 18 months ago by truebeliever2420
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