Any tool to get SNP wise stat from VCF

Question

[Govardhan Anande]

Hi,

I would like to generate SNP wise stat for all kind of SNPs(A_C, A_G, A_T, C_A, C_G, C_T, G_A, G_C, G_T, T_A, T_C & T_G) from VCF.

Is there any tool which can give me such stat.

Thanks

[MAPK]

Did you mean this: https://www.bioconductor.org/packages/3.3/bioc/html/snpStats.html

Answer 1

[Jorge Amigo]

if you bgzip compress and tabix index your vcf file, you can get that information using bcftools

bgzip file.vcf
tabix -p vcf file.vcf.gz
bcftools stats file.vcf.gz

[Govardhan Anande]

Hi Jorge,

Thanks for answer, but it calculates stat for substitution which is misleading if I am particularly interested in SNP.

For example, I have ran above commands for sample1 : I got it No. of SNP = 54233 & Substitutions = A>C 1472 A>G 5680 A>T 1414 C>A 8095 C>G 1852 C>T 8746 G>A 8748 G>C 1965 G>T 7896 T>A 1330 T>C 5645 T>G 1474 Total == 54317.

Hope you have understood my problem.

Thanks, Govardhan

[Jorge Amigo]

I've always thought that the substitutions counts were referring to snps only. good to know.

filtering snps only before running the stats module should work then:

bcftools view -v snps file.vcf.gz | bcftools stats

[Govardhan Anande]

Thanks again, I will try this then.