bash - Extracting SNPs and INDELs from a VCF using VCF tools -


how extract these snps listed in excel file this vcf file using vcf tools?

i have tried using script, took regions, not actual variants. 

#! /bin/bash  module load java module load vcftools  pvcf='yeast_combined.g.vcf.filtered.vcf' cvcf='yeast_combined.updated2.g.vcf.filtered.vcf'  #extracts snp peak regions  vcftools --vcf $pvcf --bed snp_regions.bed --recode --recode-info-all --out psnps vcftools --vcf $cvcf --bed snp_regions.bed --recode --recode-info-all --out csnps  #extracts indel region  vcftools --vcf $pvcf --bed ind_regions.bed --recode --recode-info-all --out pinds vcftools --vcf $cvcf --bed ind_regions.bed --recode --recode-info-all --out cinds


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