filter SNPs at several ranges

[Peiyuan Zhu]

I can understand the command from-bp to-bp but is it possible to filter the SNPs at several ranges if I have a table like this?

Would -snp 55013806 - 55100417, 55074849 - 55089200, ... work in this case?

Also is it possible to use a text file as input of ranges. This will be more convenient.

[Peiyuan Zhu]

Looks like snps only take in rsid. How to do it for position input only?

[Christopher Chang]

See the second sentence of the plink2 --extract documentation.

[Peiyuan Zhu]

--extract normally accepts one or more text file(s) with variant IDs (usually one per line, but it's okay for them to just be separated by spaces), and removes all unlisted variants from the current analysis. With the 'bed0' or 'bed1' modifier, the input file should be in 0-based or 1-based interval-BED format instead. For backward compatibility, 'range' is an alias for 'bed1'.

"With the 'bed0' or 'bed1' modifier, ..." is it what you're referring to?

[Peiyuan Zhu]

Still can't see why it's relevant, Could you explain a bit more?

[Christopher Chang]

You were asking how to use a "text file as input of ranges".

[Peiyuan Zhu]

I see. So I can only use bed files as input for this but not pgen?

[Christopher Chang]

No.  "BED" here refers to the "UCSC BED" interval file format, which is totally different from plink's .bed and .pgen formats.

"--extract bed0" works just fine with both plink2 .pgen and plink .bed files.