Question: How generate files plink?
0
gravatar for manubiomed20
29 days ago by
manubiomed200 wrote:

I am trying to create plink (.map and .ped) files and I am getting the message:

plink: unknown option "--"

I used the following command

plink -- vcf /home/lucasmalzoni/Documents/MT-20190821T182828Z-001/MT/Mutect2/4513.vcf.gz --recode --out ALS-MT
tool software error • 118 views
ADD COMMENTlink modified 29 days ago • written 29 days ago by manubiomed200
1
gravatar for ATpoint
29 days ago by
ATpoint23k
Germany
ATpoint23k wrote:

Whitespace between -- and vcf must be removed.


Side note: It is good practive to not exclusively use capital letters in the title as this indicates shouting, and to put in some effort into the title such as avoiding to use the same word twice within a title of four words. This simply shows some respect and appreciation towards the community which is driven entirely by volunteers and would indicate that you do not see this community as a walk-in service. Just saying, no offense intended.

ADD COMMENTlink modified 29 days ago • written 29 days ago by ATpoint23k
    plink --vcf /home/lucasmalzoni/Documents/MT-20190821T182828Z-001/MT/VCF and Plink files/4513_MT_Filtered_Samples.vcf.gz  --recode --out ALS-MT
PLINK v1.90b6.10 64-bit (17 Jun 2019)          www.cog-genomics.org/plink/1.9/
(C) 2005-2019 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to ALS-MT.log.
Options in effect:
  --out ALS-MT
  --recode
  --vcf /home/lucasmalzoni/Documents/MT-20190821T182828Z-001/MT/VCF and Plink files/4513_MT_Filtered_Samples.vcf.gz

Error: --vcf only accepts 1 parameter.
For more information, try "plink --help <flag name>" or "plink --help | more".

.

ADD REPLYlink modified 29 days ago • written 29 days ago by manubiomed200

take the space and still error.

ADD REPLYlink written 29 days ago by manubiomed200

Is this the command you used?

plink --vcf /home/lucasmalzoni/Documents/MT-20190821T182828Z-001/MT/VCF and Plink files/4513_MT_Filtered_Samples.vcf.gz --recode --out ALS-MT?

Why is there an and in the command line, I think you accidentally mixed two commands.

ADD REPLYlink written 29 days ago by ATpoint23k

This is just the name of the subfolder.

ADD REPLYlink written 29 days ago by manubiomed200

Replace whitespaces by a proper delimiter such as underscore. Plink interpretes this is two arguments, which is imho one of the many reasons why whitespaces should never be used in file or folder names in a Unix environment.

ADD REPLYlink modified 29 days ago • written 29 days ago by ATpoint23k

thank you. I changed the name of the directory and it worked.

ADD REPLYlink written 26 days ago by manubiomed200
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