Recoding lgen into Ped using plink

Question

[njbernstein]

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

[chrchang523]

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.

[njbernstein]

I'll do that. Thanks!

[njbernstein]

So I ran it with the latest build and got the same error:

/labseq/tools/plink_linux_x86_64_dev/plink   --lfile /labseq/analysis_results/projects/Nick_familial/qc/Plate3_final_report
PLINK v1.90p 64-bit (4 Nov 2015)           https://www.cog-genomics.org/plink2
(C) 2005-2015 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to plink.log.
Options in effect:
  --lfile /labseq/analysis_results/projects/Nick_familial/qc/Plate3_final_report
193671 MB RAM detected; reserving 96835 MB for main workspace.
Processing .lgen file... 4%Error: Variant 'HH_58440    HH_58440' in .lgen file has 3+ different alleles

Any ideas? @chrchang523

[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.

[chrchang523]

Error message should be fixed in the Nov 6 development build.

[Ahill]

Bumping this thread - received same error message in plink v1.9b3.32 (24 feb) in a slightly different context. plink.log was:

PLINK v1.90b3.32 64-bit (24 Feb 2016)

Options in effect:
  --lfile OExEx10K_2015.11_gtReport
  --make-bed
  --out OExEx10K_2015.11_gtReport

Processing .lgen file... Error: Variant '19_58831980' in .lgen file has 3+ different alleles.

But this variant appears to be monomorphic (all G G) in the input .lgen file:

grep 19_58831980 OExEx10K_2015.11_gtReport.lgen | cut -f3-5 -d' ' | sort -u

19_58831980 G G

Have I missed something?

[chrchang523]

Hi,

Can you send me the .log file and the .lgen fileset so I can investigate?

Answer 1

[dr.akilalshawi]

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