How to convert from csv to ped and map files?

Question

[mahir.firefox]

Hello everyone,

I'm newbie with plink, I need to do this analysis but I cannot figure out how to convert to ped and map files. I have this big document that I was able to transpose in a way that I need, but because it's a big file it takes a lot of time and I could use a help.

I use Linux. I researched that I can do it with PLINK

I have only this file (csv) in my folder.

[firefoxer@firefoxer-pc snip]$ ls plink.log transposed_file_10.csv

I tried like this...

[firefoxer@firefoxer-pc snip]$ plink --ped transposed_file_10.csv --allow-extra-chr
PLINK v1.90b6.26 64-bit (2 Apr 2022)           www.cog-genomics.org/plink/1.9/
(C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to plink.log.
Options in effect:
  --allow-extra-chr
  --ped transposed_file_10.csv

7641 MB RAM detected; reserving 3820 MB for main workspace.
Error: Failed to open .
[firefoxer@firefoxer-pc snip]$ plink --ped transposed_file.csv --map transposed_file.csv --allow-extra-chr
PLINK v1.90b6.26 64-bit (2 Apr 2022)           www.cog-genomics.org/plink/1.9/
(C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to plink.log.
Options in effect:
  --allow-extra-chr
  --map transposed_file.csv
  --ped transposed_file.csv

7641 MB RAM detected; reserving 3820 MB for main workspace.
Error: Failed to open transposed_file.csv.
[firefoxer@firefoxer-pc snip]$ 

How can I convert to ped and map files?

[4galaxy77]

Why are you using ped and map files? There's some valid reasons, but they are very old and inefficient and a different data format is usually better.

[mahir.firefox]

I'm student researcher, I'm working on a scientific paper, and this is my first time in this field.

I have SNP data for different apple varieties and I have to do PCA (Principal Component Analysis) and few more analysis (depending of other factors). My research said that I need map and ped files in order to run PLINK for analysis. If this type of files are outdated, what do you recommend to use?

[4galaxy77]

OK. csv isn't really a data format, all it says that columns are separated by commas. Please can you post a small sample in your question (edit your original question) so we can see what it looks like and how you could convert it. Thanks.

[chrchang523]

The community standard is VCF. PLINK itself has had better support for VCF than map/ped files for close to a decade.