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---
Name: Bcftools
URL: https://samtools.github.io/bcftools/
Description: >
BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF.
---
The Bcftools module parses results generated by
[Bcftools](https://samtools.github.io/bcftools/),
a suite of programs for interacting with variant call data.
Supported commands: `stats`
#### Collapse complementary substitutions
In non-strand-specific data, reporting the total numbers of occurences for both changes
in a comlementary pair - like `A>C` and `T>G` - might not bring any additional information.
To collapse such statistics in the substitutions plot, you can add the following section into
[your configuration](http://multiqc.info/docs/#configuring-multiqc):
```yaml
bcftools:
collapse_complementary_changes: true
```
MultiQC will sum up all complementary changes and show only `A>*` and `C>*` substitutions
in the resulting plot.
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