Question: Calculate heterozygosity for each SNPs in the bim file.
gravatar for mostafarafiepour
19 months ago by
mostafarafiepour70 wrote:

Hi all dear,

I have downloaded a database that is related to SNP-chip data. This database contains three files:

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So, i want to Calculate heterozygosity for each SNPs. I use plink --make-bed --file Colli_buffalo_diversity --freqx --out Coli_freqx script to calculate heterozygosity, but I encounter the following error and ask me for a map file.

(plink) [m.rafiepour222@abrii1 New_folder]$ plink --make-bed --file Colli_buffalo_diversity --freqx --out Coli_freqx
PLINK v1.90b4 64-bit (20 Mar 2017)   
(C) 2005-2017 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to Coli_freqx.log.
Options in effect:
  --file Colli_buffalo_diversity
  --out Coli_freqx

2132707 MB RAM detected; reserving 1066353 MB for main workspace.
Error: Failed to open

What is the best suggestion for my case?

Best Regard


snp snp-chip • 699 views
ADD COMMENTlink modified 19 months ago • written 19 months ago by mostafarafiepour70

Where is your follow up to this? - Calculating Heterozygosity for each SNPs. If you got the problem in the first question to work, surely you can infer how to solve this new (but related) problem?

ADD REPLYlink written 19 months ago by Kevin Blighe63k

Error: Failed to open

You have binary format (bim/bam files) acceptable by plink. Use --bfile

ADD REPLYlink modified 19 months ago • written 19 months ago by Bioinformatics_NewComer320
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