my VCF file was said to contain no header/meta data when using vcftools
Entering edit mode
7.9 years ago
CrazyB ▴ 260

New to NGS and am trying to run PLINK for association studies. One of the steps to run PLINK is to convert my VCF output from NGS variant calling pipeline into PED and MAP. Not sure why it is but when I run vcftools to convert my VCF to PED format, which runs like

vcftools --vcf file1.vcf --plink

an error message says No header or meta information. I thought my VCF has header/meta information, but

I did notice that my VCF file is formatted in the following way

## fileformat = VCFv4.1
##FILTER = <ID = ....
##FORMAT = <ID = ...

I am NOT sure if the quotation marks are at fault, but also I do not know how to remove them and still save the file as VCF. (i.e. I usually open VCF in notepad++, but when I make changes and save it as new, it's always saved as a txt, not VCF).

Thus my Questions are

(a) do I really have missing header/meta information? If yes, how do I add them back to the VCF?

(b) if it's simply due to the quotation marks so that vcftools thought my VCF does not contain header/meta info, how could I remove them but still save my file as VCF?

Any help will be appreciated. Thanks a lot.

ngs vcf PLINK vcftools • 2.9k views

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