Methods to count Number of SNPs and Novel SNPs in a Variant Calling File (.vcf) ?.

Question

[ravi.uhdnis]

Hi,

I am looking for methods to count number of Single Nucleotide Polymorphism (SNPs) in a variant calling file (.vcf). Also, what are the ways to know "Novel SNPs" in a .vcf? I have a .vcf of Human whole genome sequencing sample with 30X coverage, PE sequencing from illumina 2500 platform. Thanks is advance.

Answer 1

[Pierre Lindenbaum]

Use GATK VariantAnnotator https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_annotator_VariantAnnotator.php to fill the column ID of the VCF using a set of one or more external public VCF (dbsnp.vcf, exac.vcf, 1000g.vcf, etc...)

Then use 'bcftools filter' or 'gatk VariantFiltration' to exclude the rows having an unknown ID, and count the lines not starting with '#'.