Creation Of A .Bed File From .Txt

Question

[tom.d.brocklehurst]

I have downloaded a subset of data I need to keep from a dataset and it has saved the file as ".txt", how do I convert the .txt file to .BED file so I can use the bed file for further QC testing?

[Devon Ryan]

You'll need to post a portion of the text file to get any help. Even .bed files are text files.

[tom.d.brocklehurst]

Sure. Here's a portion of the text file:

148594_H10_1958_BC1041075    1
148594_H05_1958_BC1041082    1
120437_F01_BLOOD321047    1
120444_E12_BLOOD321899    1
120438_A04_BLOOD321231    1

[Devon Ryan]

I have no idea what those are IDs for and google only finds them in this post. You'll need to mention where you got this or what the nature of these IDs are.

[Neilfws]

BED format description here. As a minimum you require chromosome, start and end positions. Do these exist in your file? If not, you cannot convert directly.

[chrchang523]

PLINK .bed (for "binary .ped") is not the same thing as UCSC BED (for "Browser Extensible Data") format...

[Neilfws]

Right. Original questioner needs to clarify that (I see plink as a tag, but need more information than that).

[tom.d.brocklehurst]

My apologies and am using plink so the files I need are .bed. The file I have kept from the binary dataset is a .txt file and I then need to QC on the extracted data. The first QC I need to perform is a MAF (plink --file mydata --maf 0.05) but it states I cannot do this because I do not have a .ped file, so do I need to create a .ped or .bed file for this?