How Can I Count Snps In My Final Vcf Files

Question

[mostafarafiepour]

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

[cpad0112]

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

[ghada.alqubati101]

try this

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

Answer 1

[finswimmer]

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

[mostafarafiepour]

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

[mostafarafiepour]

Sorry swimmer,

Please describe the details in the photo for me.

[Pierre Lindenbaum]

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.

[mostafarafiepour]

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

ID

REF

ALT

QUAL

INFO

GT:AD:DP:GQ:PL

AND ......

[Pierre Lindenbaum]

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

Answer 2

[finswimmer]

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

[Kash]

Hi finswimmer,

Can you please tell me how to count per sample variants from a multi sample vcf file? (how many 1/1, 0/1 SNPs are their per sample)

Thank you

Answer 3

[dario.galanti92]

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}'

[Pierre Lindenbaum]

I'm sorry but this is wrong.

> echo "chr1 123 . A C,<INDEL>,G" | awk '{if ($4~/[ATCG]/ && $5~/[ATCG]/) {c++}} END {print c}'
1

better use:

bcftools view --no-header -G -m 2 -M 2 --types snps input.vcf.gz | wc -l

[dario.galanti92]

Yes, that was indeed wrong, apologies. I fixed it now.

Answer 4

[4galaxy77]

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

Answer 5

[ghada.alqubati101]

try this

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

[Pierre Lindenbaum]

why do you output %POS ?

 bcftools query -f 'x' input.vcf | wc -c