I am sorry although there are so many questions on this query i could not find the relavant answer. I used vcftools to extract only snps from vcf file using below command
command: vcftools --vcf variantsfilterQDPMQ.vcf --remove-indels --recode --recode-INFO-all --out onlysnps
I got the vcf file which has the information about each nucleotide with snp as well as without snp. I want vcf file only with snp information alone.
I wrote a perl program, its taking lot of time since i got a big vcf file which is 10gb..
Thank you all