diff --git a/CHANGELOG.md b/CHANGELOG.md index bcbbe35f12..e78c8eb278 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,7 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [1660](https://github.com/nf-core/sarek/pull/1642) - Add `--length_required` for minimal reads length with `FASTP` - [1663](https://github.com/nf-core/sarek/pull/1663) - Massive conda modules update - [1664](https://github.com/nf-core/sarek/pull/1664) - Check if flowcell ID matches for read pair -- [1680](https://github.com/nf-core/sarek/pull/1682) - Add `bcftools_norm` in `POST_VARIANTCALLING` for normalization of all vcf files or for concatenated germline vcfs +- [1680](https://github.com/nf-core/sarek/pull/1682) - Add `bcftools_norm` in `POST_VARIANTCALLING` for normalization of all vcf files; edit vcf_concatenate_germline subworkflow - [1730](https://github.com/nf-core/sarek/pull/1730) - Enable Harshil Alignment™️ in VS Code workspace settings ### Changed diff --git a/README.md b/README.md index 33892e0a6b..e07cd591f1 100644 --- a/README.md +++ b/README.md @@ -181,6 +181,7 @@ We thank the following people for their extensive assistance in the development - [Szilveszter Juhos](https://github.com/szilvajuhos) - [Tobias Koch](https://github.com/KochTobi) - [Winni Kretzschmar](https://github.com/winni2k) +- [Patricie Skaláková](https://github.com/Patricie34) ## Acknowledgements diff --git a/docs/output.md b/docs/output.md index 6204ada6a5..c24f493a5e 100644 --- a/docs/output.md +++ b/docs/output.md @@ -855,6 +855,19 @@ Germline VCFs from `DeepVariant`, `FreeBayes`, `HaplotypeCaller`, `Haplotyper`, +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. + +
+Normalized VCF-files for normal and tumor samples + +**Output directory: `{outdir}/variantcalling/normalized//`** + +- `..norm.vcf.gz` and `..norm.vcf.gz.tbi` + - VCF with tabix index + +
+ + ## 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`.