edit plink command to to give me only 0,1,2 genotypes

[Ana Marija]

Hello,

how to edit this plink command:

plink --noweb --file merged --extract $snpFile --maf .001 --geno .05 --recode 12 --out merged_forldmax_pre0

to give me genotypes in form: 0,1,2

Thanks

Ana

[Christopher Chang]

"--recode A" and "--recode A-transpose" generate text files with 0-1-2-encoded genotypes.

[Ana Marija]

Hello,

thanks for the help. Right now using

plink --noweb --file merged --extract $snpFile --maf .001 --geno .05 --recode A-transpose --out final_$snpFile

I am getting result in this form:

  NA20826_NA20826 NA20828_NA20828
1               0               1
2               0               1
3               0               1
4               0               1
5               0               1
6               0               1

I would need to get result in this form:

  NA20814 NA20815 NA20816 NA20819 NA20826 NA20828
1       0       0       1       1       0       0
2       2       2       2       2       2       2
3       0       0       0       0       0       0
4       0       0       0       0       0       0
5       0       0       0       0       0       0
6       0       0       0       0       0       0

How do I do that?

Thanks

Ana

--
You received this message because you are subscribed to the Google Groups "plink2-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to plink2-users...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Ana Marija]

Hi Christopher,

is there is anything I can put in this plink command:

plink --noweb --file merged --extract $snpFile --maf .001 --geno .05 --recode A-transpose --out final_$snpFile

to have column named NA20826 instead of NA20826_NA20826 (see previous message)?

Thanks

Ana

[Christopher Chang]

No, but this modification should be straightforward to do with a shell script.

On Wednesday, January 16, 2019 at 5:48:23 AM UTC-8, Ana Marija wrote:

Hi Christopher,

is there is anything I can put in this plink command:

plink --noweb --file merged --extract $snpFile --maf .001 --geno .05 --recode A-transpose --out final_$snpFile

to have column named NA20826 instead of NA20826_NA20826 (see previous message)?

Thanks

Ana

To unsubscribe from this group and stop receiving emails from it, send an email to plink2-users+unsubscribe@googlegroups.com.

[Ana Marija]

Thank you!

To unsubscribe from this group and stop receiving emails from it, send an email to plink2-users...@googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

--

You received this message because you are subscribed to the Google Groups "plink2-users" group.

To unsubscribe from this group and stop receiving emails from it, send an email to plink2-users...@googlegroups.com.

[bassu]

Hi Christopher,

Adding to this .

Is there a away where I can get only 0 and 1 as genotypes. What I need is convert all 2 ->1 and then do assoc testing ?

[DaveA]

Hi Bassu, isn't that a dominance model that you can test with the --model flag?

Dave