need command to match snps

[Genetics189291]

I want to match the snps (rsid) from a file I have to my dataset so that it only matches those snps. I've tried several commands and it's just not doing it

[AimSmall]

I want to match the snps (rsid) from a file I have to my dataset so that it only matches those snps. I've tried several commands and it's just not doing it

plink(version number) --bfile "dataset" --keep extractlist --make-bed --out "your sample"

[Genetics189291]

I want to match the snps (rsid) from a file I have to my dataset so that it only matches those snps. I've tried several commands and it's just not doing it

plink(version number) --bfile "dataset" --keep extractlist --make-bed --out "your sample"

I should have mentioned it's a .txt file it's formatted in this way 

rs6668 
rs2134532

etc 

when I use that command it tells me line 1 of keep file has fewer tokens then expected

[AimSmall]

My bad.... keep is for samples

Use --snps

Think you can put a filename after the --snps

Code:

Multiple ranges
--snps <variant ID(s)/range(s)...>
--exclude-snps <variant ID(s)/range(s)...>

--snps accepts a collection of individual variant IDs and variant ranges. For example,

--snps rs1111-rs2222, rs3333, rs4444

tells PLINK to load all variants between rs1111 and rs2222 inclusive, as well as rs3333 and rs4444. (Syntax works the same way as --chr. If your variant IDs contain dashes, you'll want to use the --d flag as well.) If rs1111 and rs2222 are on different chromosomes i < j, then all variants on chromosomes numbered between i and j are loaded, as well as the last variants on chromosome i and the first variants on chromosome j. (You can exclude some intermediate chromosomes by combining --snps with --not-chr.)

[AimSmall]

plink --bfile data --extract snps.txt --recodeA

[Genetics189291]

My bad.... keep is for samples

Use --snps

Think you can put a filename after the --snps

Code:

Multiple ranges
--snps <variant ID(s)/range(s)...>
--exclude-snps <variant ID(s)/range(s)...>

--snps accepts a collection of individual variant IDs and variant ranges. For example,

--snps rs1111-rs2222, rs3333, rs4444

tells PLINK to load all variants between rs1111 and rs2222 inclusive, as well as rs3333 and rs4444. (Syntax works the same way as --chr. If your variant IDs contain dashes, you'll want to use the --d flag as well.) If rs1111 and rs2222 are on different chromosomes i < j, then all variants on chromosomes numbered between i and j are loaded, as well as the last variants on chromosome i and the first variants on chromosome j. (You can exclude some intermediate chromosomes by combining --snps with --not-chr.)

I tried this but it didn't seem to work 

I tried the command below which also didn't seem to work, I can go through it one by one and filter it but it would take a long time to do

[AimSmall]

Post your snp restriction file

[nomad01]

do you mean the " --extract snp.txt " command?

[Genetics189291]

Post your snp restriction file

will do

[Genetics189291]

do you mean the " --extract snp.txt " command?

I tried this and it seemed not to work, I checked the files and it didn't execute the command, I also tried awk but no luck

[nomad01]

do you mean the " --extract snp.txt " command?

I tried this and it seemed not to work, I checked the files and it didn't execute the command, I also tried awk but no luck

it should be working, bed/bim/fam, plink2.exe and snp.txt should all be in the same folder

[Genetics189291]

do you mean the " --extract snp.txt " command?

I tried this and it seemed not to work, I checked the files and it didn't execute the command, I also tried awk but no luck

it should be working, bed/bim/fam, plink2.exe and snp.txt should all be in the same folder

I’m gonna try when I get home