diff --git a/docs/output.md b/docs/output.md index c24f493a5e..e34668b051 100644 --- a/docs/output.md +++ b/docs/output.md @@ -855,6 +855,8 @@ Germline VCFs from `DeepVariant`, `FreeBayes`, `HaplotypeCaller`, `Haplotyper`, +### 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.
@@ -867,7 +869,6 @@ All VCFs from `DeepVariant`, `FreeBayes`, `HaplotypeCaller`, `Haplotyper`, `Mant
- ## 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`.