.vcf has fewer tokens than expected error

[sererenaa]

In part 2, when we convert from vcf to Plink format, I get an error:

Any advice to get around this? I end up with temporary files because of this & the rest of the tutorial is not functioning the way it should.

[sjhangiani12]

Hi were you able to find a solution to this?

[Maommmy]

Have you found a solution to this problem? I get an error too...

[FedericoBottoni]

I got this more generic error. I tried to download the vcf file 4 times but I always got the same issue [PLINK v1.90b6.24 64-bit]

[MaYueyangRuby]

I met the same problem and solved it today. Look at the 217969 line (the line number reported in the error) of your vcf file, this line may not be intact.

[mpage21]

#17
I believe the attached issue has the answer to the cause of these errors.

[licong-198]

I met the same problem and solved it today. Look at the 217969 line (the line number reported in the error) of your vcf file, this line may not be intact.
My file is large, and this line is incomplete. Can I use 'sed' to delete it？

[echolihuifang]

我遇到了同样的问题，今天解决了它。查看 vcf 文件的217969行（错误中报告的行号），此行可能不完整。

您好，请问您是如何解决的，我也遇到了相同的报错。谢谢！

[Hammerklavier-cn]

Maybe you can try to check the integrity of the file. .gz should have this function. As you know, connection between Asia and US is vulnerable, resulting in me running into the same problem. I rent an overseas server in south America, downloaded the file, and transferred it back to Asia through scp. BTW, don't forget to execute a md5 check.