VCF does not have correct column number

[Zepeng-Mu]

Hi, I am using checkVCF and got the error Line [ 1 ] does not have correct column number, exiting!. I checked the columns by reading first several lines into python and split them by \t, which gave me the same column number. I did not encounter this when processing other datasets.
How can I fix this?
Many thanks

[Zepeng-Mu]

So changing this line 212 fd = ln.strip().split() to split('\t') seem to solve my problem. Although I do not need to change the code for reading the header line.

[zhanxw]

Thanks for the report. The VCF specification requires \t instead of white space. So I used it in the script.

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On Mar 18, 2019, at 1:37 PM, Zepeng Mu ***@***.***> wrote: So changing this line 212 fd = ln.strip().split() to split('\t') seem to solve my problem. Although I do not need to change the code for reading the header line. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.