Background: Usually we grouped the genomic variants into different types, like SNP, insertion, deletion, Transposable element.
I would like to get some primary statistics, like frequency or counts, for different types of such genomic variants, by vcftools. And also I want to export this genomic variant data for population genetic studies, for example, exporting allele frequency data only for SNPs or Indels.
My question: I want to know if there are tools/strategies to divide SNP variants from indel variants in the same VCF file (only snp and indel there), and keep them into different vcf files. I do my study depending on VCF and VCFTools.
I think your suggestions are really valuable for me and who are depending on VCF format. Thanks in advance.
This question has ever been asked in VCFTools-help mailing list. But, I have not gotten any replies.