creating ped file from txt file

Question

[forever]

Hi, I have genotyping file "x1.txt"with the below header:

SNP Name Sample ID Allele1 - Top Allele2 - Top GC Score SNP

chr1:109457160 2 C C 0.8609 [T/G]

I need to convert this file to ped to process it in Plink. This is what I find in Plink tutorial:

To output a file in the LGEN format, use the command --recode-lgen which generates files

plink.lgen plink.fam plink.map

so I try the new line in plink: plink --recode-lgen x1.lgen

But I got the following error: The first parameter must be a flag.

I appreciate any help. Thank you

[breckuh]

Did you ever solve this? I have a "txt" file in the same format and am having trouble figuring out a column:

What does SNP mean in data from an Illumina MetaboChip final report?