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title: "Variant Calling"
canonical: "https://help.biobam.com/space/OUM3/3675852692/Variant%20Calling"
format: markdown
---
Variant calling is the process by which we identify variants (such as SNPs, insertions or deletions) from sequence data. This data, which is stored in a VCF file, can be used to  annotate  variants, if you are interested in the genetic and coding consequences of each mutation, and to  associate variants to phenotypic traits , in order to know if a variant is significantly related to a characteristic. There are different algorithms specifically designed to achieve this goal: BCFtools :  this is a  widely-used  variant calling tool, especially among non-human species, which is characterized by its small time of execution and its precision. Freebayes :  this tool is characterized by its capability to use it with polyploid genomes.