Question: Calculate heterozygosity for each SNPs in the bim file.
0
gravatar for mostafarafiepour
10 days ago by
mostafarafiepour60 wrote:

Hi all dear,

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

enter image description here

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)             www.cog-genomics.org/plink/1.9/
(C) 2005-2017 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to Coli_freqx.log.
Options in effect:
  --file Colli_buffalo_diversity
  --freqx
  --make-bed
  --out Coli_freqx

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

What is the best suggestion for my case?

Best Regard

Mostafa

snp snp-chip • 140 views
ADD COMMENTlink modified 10 days ago • written 10 days ago by mostafarafiepour60
1

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 10 days ago by Kevin Blighe35k

Error: Failed to open Colli_buffalo_diversity.map

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

ADD REPLYlink modified 9 days ago • written 9 days ago by Bioinformatics_NewComer320
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