File Conversion from VCF to .bed format (goal is to use it in the admixture)

[Safiqul Islam]

Dear All

I am new plink user. 

I am trying to convert vcf file to bed format. command was  plink --vcf M29F30_BiSnps.recode.vcf --make-bed --recode --write-covar --out ./; and it looks it worked. But of course sex information was not there because i did not add then, Could you please suggest how can I specify the sex information (Male=ZZ and Female ZW), I tried via text file like this, definitely this wrong. could you please suggest me how can I add sex information in ped file. 

L63604 male

L63605 Female 

L63591 male

L63592 male

L63600 male

L63601 male

L57007 male

L63620 male

Thank you in an advance 

best

Safz

[Christopher Chang]

See the --update-sex flag.

[Chris Chang]

If you want to use a single ID column with plink --update-sex:

* Use plink 2.0 instead of plink 1.9.

* Add a "#IID SEX" header column to your --update-sex file.

Then,

  "plink2 --vcf M29F30_BiSnps.record.vcf --update-sex <sex info file> --make-bed --out ..."

should work.

On Fri, Feb 5, 2021 at 11:32 AM Safiqul Islam <safi...@gmail.com> wrote:

Dear Chang

I am trying to update the sex information but i did not get couple of things.

my pop file is like this 

L63604 M

L63605 F

L63591 M

L63592 M

L63600 M

but manual says i have to add two more columns of FIDs and IIDs, I dont get what I have to add here.

could you please suggest a sample pop file please or reply to this email please.

best

Safi

On Fri, Feb 5, 2021 at 8:28 PM Safiqul Islam <safi...@gmail.com> wrote:

D

--update-sex expects a file with FIDs and IIDs in the first two columns, and sex information (1 or M = male, 2 or F = female, 0 = missing) in the (n+2)th column

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--

Safiqul Islam

Founder & CEO, wildmentor (http://www.wildmentor.org/)

Scientific Assistant at Senckenberg Naturhistorische Sammlungen Dresden (http://www.senckenberg.de/)

Doctoral Student (Phylogeography-Ornithology) at Ludwig-Maximilians-Universität München (http://www.uni-muenchen.de/)

--

Safiqul Islam

Founder & CEO, wildmentor (http://www.wildmentor.org/)

Scientific Assistant at Senckenberg Naturhistorische Sammlungen Dresden (http://www.senckenberg.de/)

Doctoral Student (Phylogeography-Ornithology) at Ludwig-Maximilians-Universität München (http://www.uni-muenchen.de/)

[Christopher Chang]

oops, "header column" should be "header line".  Anyway, your --update-sex file should look something like

#IID  SEX

L63604  M

L63605  F

L63591  M

L63592  M

L63600  M

...

[Chris Chang]

1. Again, you need to use plink 2.0 (so your command line should start with "plink2 ..." instead of "plink ...") for the single-ID-column --update-sex file to work.

2. Since you are working with a nonhuman chromosome set, you need to use the --chr-set flag to describe the chromosome set.

On Fri, Feb 5, 2021 at 12:38 PM Safiqul Islam <safi...@gmail.com> wrote:

Dear Chang

sorry for disturbing you, Really sorry.

My command was like this: $ plink --vcf M29F30_BiSnps.recode.vcf --update-sex ./SexInfo-M1-F2.txt --make-bed --out ./

Population file was like this.

#IID SEX
L63604 M
L63605 M
L63608 M
L63609 M
L56980 M

For the chromosome: I want to modify only sex chromosomes.

Inside the vcf file sex chromosome X=29 and Y=30.

I got this error. Could you please suggest to me how I can fix it.

Output was

Logging to ./.log.

Options in effect:

  --make-bed

  --out ./

  --update-sex ./SexInfo-M1-F2.txt

  --vcf M29F30_BiSnps.recode.vcf

16384 MB RAM detected; reserving 8192 MB for main workspace.

Error: Invalid chromosome code '29' on line 12 of .vcf file.

(This is disallowed for humans.  Check if the problem is with your data, or if

you forgot to define a different chromosome set with e.g. --chr-set.)

Thanks a lot for your kind help. I spent couple of days to solve this issue,you are really great , Thanks a lot for your help

best

Safi

To view this discussion on the web visit https://groups.google.com/d/msgid/plink2-users/fbdfd29e-5e56-4f36-be5c-a1cec0622a70n%40googlegroups.com.

[Chris Chang]

Actually, the biggest issue here is that I forgot to mention that you need to REVERSE male/female if you want plink to work with species with ZW sex-determination.  Sorry about that; hopefully this isn't too much of a pain.

After you have done that in your --update-sex file, "--chr-set 28" should work.  This makes 29 get treated as chrX and 30 get treated as chrY... which ends up working the same way as 29=Z, 30=W if the sexes are reversed.

On Fri, Feb 5, 2021 at 12:59 PM Safiqul Islam <safi...@gmail.com> wrote:

Dear Chang

I read the that looks really complex to me. I am working with birds. for the birds Male ZZ and females has ZW.

I am using ref based genome. here I am only using sex chromosomes. and Chromosome number 29=ZZ and 30=ZW

plink2 --vcf M29F30_BiSnps.recode.vcf --update-sex ./SexInfo-M1-F2.txt --chr-set --make-bed --out ./

what I should specify here "--chr-set " after this please please help. 

thank you in an advance