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Old 02-20-2017, 01:15 PM   #1
Location: USA

Join Date: Apr 2014
Posts: 16
Default Counting of SNPs in different genomic regions

After annotating the SNP.vcf files using SnpEff v 4.2, I would like to count how many SNPs are found in different genomic regions such as upstream, gene, exon, intron, CDS, 5' UTR, 3' UTR, downstream and intergenic. To perform the SNPs count, I am looking for a program or perl- or python script for few days in different forums. I have annotated SNP.VCF and gene.txt file obtained from SNpEff. Can anyone help me - how can I count the number of SNPs found in different genomic regions? I would highly appreciate your help. Thanks
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