Calculate heterozygosity for each SNPs in the bim file.

Question

[mostafarafiepour]

Hi all dear,

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

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

[Kevin Blighe]

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?

[Bioinformatics_NewComer]

Error: Failed to open Colli_buffalo_diversity.map

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