Question: File conversion: lgen to ped and map
0
gravatar for Tastulek
3.1 years ago by
Tastulek0
Tastulek0 wrote:

Hello BioStar Community:

I am having a problem in converting Plink lgen to ped and map formats.

The columns of my lgen file:

[Header]

GSGT Version 1.9.4

Processing Date 7/22/2016 3:32 PM

Content GxG_ComprehensiveArray_v1_10070487_A2.bpm

Num SNPs 739437

Total SNPs 758221

Num Samples 1

Total Samples 2112

[Data]

Sample ID SNP Name Allele1 - Plus Allele2 - Plus

GRC15631334 105SNP6248RT_C A A

GRC15631334 108SNP8860FA_G G G

GRC15631334 10SNP12636FC_T C C

.......................................................................................

When the command

plink --lfile mydata --recode

was executed, the following error message appeared:

@----------------------------------------------------------@ | PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| | For documentation, citation & bug-report instructions: | | http://pngu.mgh.harvard.edu/purcell/plink/ | @----------------------------------------------------------@

Web-based version check ( --noweb to skip )

Recent cached web-check found... OK, v1.07 is current

+++ PLINK 1.9 is now available! See above website for details +++

Writing this text to log file [ plink.log ]

Analysis started: Tue Sep 27 10:04:58 2016

Options in effect:

--lfile mydata

--recode

ERROR: No file [ mydata.map ] exists.

How could the issue be solved?

snp genome software error • 1.5k views
ADD COMMENTlink modified 2.9 years ago by forever80 • written 3.1 years ago by Tastulek0

I have the same problem. Please your help. Regards

ADD REPLYlink written 2.9 years ago by forever80
1

Have a look as the structure of lgen file at https://www.cog-genomics.org/plink2/formats#lgen . It has to be accompanied by a .fam and .map file.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by akang90
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