Question: Help regarding variant filtration and variant density calculation
2.6 years ago by
mirza • 80
mirza • 80 wrote:
I have completed variant calling and annotation and I need help with the following analysis. Is it possible to do the following analysis with my vcf files using vcftools or snpsift or bedtools?
- Count the heterogygous SNPs according to different class i.e. C/T; T/C; etc
- Calculate variant density (for both SNPs and Indels, seperately) in different regions i.e. exonic region, intronic region, genes, intergenic region?
- Is it possible to filter variant data and generate separate .vcf files on the basis of the region annotated i.e. I want to generate separate .vcf files for variants in exon, intron, intergenic region?
Please guide me to the right command.
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