Perl script

[mmmm]

could I get the perl script that can be used to determine the effect of SNPs when comparing large number of samples-
I have (output.vcf) and would like to get (snp_report.txt) so it can easily show difference between strains

[dGho]

You question is a bit vague. What specifically are you looking to include in the snp report? the number or snps per sample?

[mmmm]

the script with the output vcf file takes the information from the reference fasta and annontation gff files to determine if the snps occur within a gene and shows the snp effect (silent, indel, ...)

the command should be like this:

script ref.fn ref.gff vcf file > snp-report output file

the output file contains the following 6 columns:
chrom pos ref nucleotide snp(in vcf) gene name snp status

[dpryan]

Presumably that's either variant effect predictor or snpeff.