Hello all,
I'm trying to convert .lgen into ped files using plink. However, plink won't read my lgen file all the way. I run
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
•
written
by
njbernstein •
1 answer
Hi every one
I tried to make PED&MAP files by PLINK from three files that I made it .lgen ,.map &.fam So,error appeared
Error: Variant 'ARS-BFGL-BAC-27364' in .lgen file has 3+ different alleles.
So,the command that I used it ./plink --lfile rustaqi22 --cow --recode
Moreover,example below of rows of my .lgen file
Rustaqi 88 ARS-BFGL-BAC-10172 B B Rustaqi 88 ARS-BFGL-BAC-1020 A B Rustaqi 88 ARS-BFGL-BAC-10245 B B
Could any one advice how to deal with this point?
Thanks
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Can you check whether the latest plink build produces the same error message? I seem to recall fixing an error message like this (it's supposed to report the variant ID, not the sample ID) sometime within the last year or so.
I'll do that. Thanks!
So I ran it with the latest build and got the same error:
Any ideas? @chrchang523
Okay, I will take a look at the .lgen-processing code later today; there must be a few error messages I failed to fix the last time I was rummaging around there (a variant ID should never have whitespace in the middle so this is definitely an error on my end). I'll reply again here when a development build with the fixed error message is posted to the website.
Error message should be fixed in the Nov 6 development build.
Bumping this thread - received same error message in plink v1.9b3.32 (24 feb) in a slightly different context. plink.log was:
But this variant appears to be monomorphic (all G G) in the input .lgen file:
Have I missed something?
Hi,
Can you send me the .log file and the .lgen fileset so I can investigate?