Hello,

the total number you get by counting the lines in the vcf excluding the header lines.

$ grep -v "^#" input.vcf|wc -l

fin swimmer

Hello mostafarafiepour,

you've started with one question. In the meantime there are three :)

1. How to read a vcf file

This is a very basic question. So you need starting some literature:

• Wikipedia
• the official specs (already posted by Pierre Lindenbaum )
• Have a look into the header of your file. Lot's of explanations are there

If you doesn't understand any of the explanations, don't worry to ask.

2. How to count the variants in a vcf (your original question)

We already worked on this.

3. Is the resulted number of (2) correct?

Well, that's quite hard to say without knowing anything about your genome. How large is it? Is there a high diversity between individuals? As we just have the total number of different variants in all of your samples, it might be better to get a per sample count. The output of bcftool stats (as suggested by cpad0112 ) might be useful or have a look at this thread, especially the answers by Pierre and me.

fin swimmer

Here is a quick way to count biallelic SNPs in vcf.gz files (use "cat" instead of "zcat" for uncompressed vcf files):

zcat input.vcf.gz | awk '{if ($4~/^[ACGT]$/ && $5~/^[ACGT]$/){c++}} END {print c}'

If all your variants in the vcf are SNPS, then a very quick way is to first index and then index again with the -n flag.

bcftools index data.vcf 
bcftools index -n data.vcf

try this

bcftools query -f '%POS\n' file.vcf.gz | wc -l