This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How generate files plink?

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
software-error plink
• 3,290 views • link
updated by Ram Ram • written by manubiomed20 • manubiomed20

1 answer

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.

• 0 views • link
written by ATpoint ATpoint 
    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".

.

• 0 views • link
written by manubiomed20 • manubiomed20

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.

• 0 views • link
written by ATpoint ATpoint

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.

• 0 views • link
written by ATpoint ATpoint

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

• 0 views • link
written by manubiomed20 • manubiomed20

Log in to answer this question.

More posts like this