Question: Recoding lgen into Ped using plink
0
gravatar for njbernstein
5.1 years ago by
njbernstein40
United States
njbernstein40 wrote:

 

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

illumina final report plink • 2.5k views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 5.1 years ago by njbernstein40

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.

ADD REPLYlink modified 12 months ago by _r_am31k • written 5.1 years ago by chrchang5237.4k

I'll do that. Thanks!

ADD REPLYlink modified 12 months ago by _r_am31k • written 5.1 years ago by njbernstein40

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

ADD REPLYlink modified 12 months ago by _r_am31k • written 5.1 years ago by njbernstein40

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.

ADD REPLYlink modified 12 months ago by _r_am31k • written 5.1 years ago by chrchang5237.4k

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

ADD REPLYlink written 5.1 years ago by chrchang5237.4k

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?

ADD REPLYlink modified 12 months ago by _r_am31k • written 4.7 years ago by Ahill1.9k

Hi,

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

ADD REPLYlink written 4.7 years ago by chrchang5237.4k
0
gravatar for dr.akilalshawi
4.5 years ago by
dr.akilalshawi0 wrote:

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

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by dr.akilalshawi0
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