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Patricie34 committed Dec 4, 2024
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Expand Up @@ -855,6 +855,8 @@ Germline VCFs from `DeepVariant`, `FreeBayes`, `HaplotypeCaller`, `Haplotyper`,

</details>

### Normalization

All VCFs from `DeepVariant`, `FreeBayes`, `HaplotypeCaller`, `Haplotyper`, `Manta`, `bcftools mpileup`, `Strelka`, or `Tiddit` are normalized with `bcftools norm`. The field `SOURCE` is added to the VCF header to report the variant caller.

<details markdown="1">
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</details>


## Variant annotation

This directory contains results from the final annotation steps: two tools are used for annotation, [snpEff](http://snpeff.sourceforge.net/) and [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html). Both results can also be combined by setting `--tools merge`.
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