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?
I have the same problem. Please your help. Regards
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.