Error: Missing header line in .vcf file.

[Henry Bigelow]

Hi,

Could anyone help out with the following:

$ plink --vcf whi.some.annot.vcf.gz --allow-extra-chr --make-bed --geno 0.1 --out whi.some.annot

PLINK v1.90b3.31 64-bit (3 Feb 2016)       https://www.cog-genomics.org/plink2

(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3

Logging to whi.some.annot.log.

Options in effect:

  --allow-extra-chr

  --geno 0.1

  --make-bed

  --out whi.some.annot

  --vcf whi.some.annot.vcf.gz

516830 MB RAM detected; reserving 258415 MB for main workspace.

Error: Missing header line in .vcf file.

That is all the error message that I get.  Is there some way to check the vcf file and get a more informative error message?

Thanks,

Henry

[Christopher Chang]

"zcat whi.some.annot.vcf.gz | head" should decompress and display the top lines.

[Henry Bigelow]

Hi Chris,

Thanks for your reply.  But, once I look at the vcf header (though I use bcftools view -h for that), how do I know which line should be there but isn't?  There is no detail in PLINK's error message about what is missing.

Thanks,

Henry

[Christopher Chang]

PLINK expects a sequence of header lines starting with '##', followed by one starting with '#CHROM'.  All other details are ignored.

(If you have a BCF2 file, that must be loaded with --bcf instead.)

[Henry Bigelow]

Great!  It turned out I had a bcf file, so when I switched to --bcf, it worked.