Convert ped/bed into CSV/text file
1
0
Entering edit mode
9 months ago

Hello everyone! I have preprocessed SNP data file after using PLINK in BED format. I need to carry out feature selection and hence need to import them into CSV/TXT format. Please suggest me how to do this conversion. Thank you in advance.

GWAS Machine Learning plink • 879 views
0
Entering edit mode

BED file is just a tab-separated text file, you could open it with a normal text editor or MS Excel

0
Entering edit mode

But BED file is a binary compressed file. We can't read it.

0
Entering edit mode

Thank you for the useful information. I am now faced with another problem. I need to convert all the files for work from png to pdf format. I don’t understand how to do this, nothing happens.

0
Entering edit mode

It seems complicated at first sight. Somehow I found a website https://pdfchef.com/ and decided to find out about the conversion process. Thanks to the program, I was able to convert my documents to other formats. A file editor is also available.

0
Entering edit mode

Thanks, I'll try.

1
Entering edit mode
6 months ago
Ram 34k

IIRC there are multiple "BED" formats in our field. The BED that husensofteng refers to is the UCSC BED format, which is indeed tab delimited text. As for plink's bed, it's just the fam file combined with transposed and split VCF GT fields (I think).

To convert this to a pain text file, see this post: How To Convert The Bed File To Ped File

plink --bfile input.bed --recode --tab --out output.ped.tsv

0
Entering edit mode

Oops, just saw that this post is 9 weeks old.