How Can I Count Snps In My Final Vcf Files

Question: How Can I Count Snps In My Final Vcf Files

23 months ago by

Hi all,

I have a VCF file that containing 50 samples, i want to count the number of SNPs. My organism is non-model, So it does not have the chromosome.

Now, How can i count the number of SNPs for all 50 samples with this VCF?

Best Regard

Mostafa

snp • 2.2k views

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modified 23 months ago by finswimmer ♦ 13k • written 23 months ago by mostafarafiepour • 70

run bcftools stats on vcf. It would summarize the VCF with most of the details you need.

ADD REPLY • link modified 23 months ago • written 23 months ago by cpad0112 ♦ 13k

23 months ago by

finswimmer ♦ 13k

Germany

finswimmer ♦ 13k wrote:

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

ADD COMMENT • link modified 23 months ago • written 23 months ago by finswimmer ♦ 13k

23 months ago by

finswimmer ♦ 13k

Germany

finswimmer ♦ 13k wrote:

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

ADD COMMENT • link written 23 months ago by finswimmer ♦ 13k

Hi swimmer,

Many thanks for your reply, I've done it and gave me a number(20546654). But I do not know how correct this number is?

Code i use:

grep -v "^#" Final_VCF_50Sample.vcf|wc -l

ADD REPLY • link modified 23 months ago by finswimmer ♦ 13k • written 23 months ago by mostafarafiepour • 70

Sorry swimmer,

Please describe the details in the photo for me.

enter image description here

ADD REPLY • link written 23 months ago by mostafarafiepour • 70

Please describe the details in the photo for me.

how is it related to your original question ? Are you sure you're using the correct terms ?

Each line of the VCF is a VARIANT. A Variant can be a SNP or an INDEL or etc...

The intersection of the Variant and the Samples' names is a GENOTYPE.

ADD REPLY • link written 23 months ago by Pierre Lindenbaum ♦ 129k

Yes, maybe I did not ask the exact question.

I want to know what the meaning of any of the terms in the picture is?

for example:

CHROM

POS

REF

ALT

QUAL

INFO

GT:AD:DP:GQ:PL

AND ......

ADD REPLY • link modified 23 months ago • written 23 months ago by mostafarafiepour • 70

I want to know what the meaning of any of the terms in the picture is?

https://samtools.github.io/hts-specs/VCFv4.3.pdf

ADD REPLY • link written 23 months ago by Pierre Lindenbaum ♦ 129k

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