I'm trying to convert .lgen into ped files using plink
However, plink won't read my lgen file all the way.
plink --lfile /labseq/analysis_results/projects/Nick_familial/qc/Plate3_final_report
And my error is:
PLINK v1.90b2i 64-bit (8 Sep 2014) https://www.cog-genomics.org/plink2 (C) 2005-2014 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to plink.log. 193671 MB RAM detected; reserving 96835 MB for main workspace. Processing .lgen file... 4%Error: Variant 'blah blah' in .lgen file has 3+ different alleles.
'blah blah' is just the subject names repeated twice as it is for all the rows, so I can't track down the problem. I also ran cut -f-5 /labseq/analysis_results/projects/Nick_familial/qc/Plate3_final_report.lgen > tmp && mv tmp /labseq/analysis_results/projects/Nick_familial/qc/Plate3_final_report.lgen
As I though there might be another column, but I got the same bug when I reran it.
Any ideas on debugging? Any help would be much appreciated