PLINK: invalid alternate allele on .vcf file

Question

[Matteo]

Hi,

When trying to convert a vcf file to a bed format with PLINK I get the following error:

Error: Invalid alternate allele on line 679 of .vcf file.

I am a frequent user of PLINK and this is the first time I get this. Does anyone have any idea what may cause such an error? Thanks in advance!

Matteo

[Ram]

Please print the 679th line of the VCF file (counted with and without header) and show it to us:

sed -n '679p' file.vcf | cut -f1-8
grep -v "^#" file.vcf | sed -n '679p' | cut -f1-8

EDIT: To be more efficient, stop processing at line 680 or as early as possible.

sed -n '679p;680q' file.vcf | cut -f1-8
grep -m679 -v "^#" file.vcf | tail -n 1 | cut -f1-8