Closed:SHAPEIT4 incorrect number of columns

Question

[michael.turner]

Hello, I hope that this is not too basic a question.

I am trying to phase a dataset in SHAPEITv4. QC was done in plink by a colleague, and I converted it to .vcf format, compressed it and produced the necessary index file for SHAPEITv4 to read.

I am getting an error at the VCF parsing stage:

ERROR: Parsing line 0 : incorrect number of columns, observed: 1 expected: 3

I am not certain where it is expecting to see three columns. The .vcf header should have one, and the body at least eight. There is obviously something that I am not aware of, and I would be very grateful for any pointers.

Thanks,

Mike