From c2ffb57cd4fc3d4aa9500bccb9f5a9e054134e6d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=9CMarcel-Mueck=E2=80=9D?= <“mueckm1@gmail.com”>
Date: Thu, 5 Oct 2023 16:37:25 +0200
Subject: [PATCH] added required repos to requirements

---
 deeprvat/annotations/README.md | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/deeprvat/annotations/README.md b/deeprvat/annotations/README.md
index 2e576a02..5b686882 100644
--- a/deeprvat/annotations/README.md
+++ b/deeprvat/annotations/README.md
@@ -11,12 +11,20 @@ The pipeline uses left-normalized bcf files containing variant information, a re
 
 ## Requirements 
 BCFtools as well as HTSlib should be installed on the machine, 
-[CADD](https://github.com/kircherlab/CADD-scripts/tree/master/src/scripts) as well as [VEP](http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html) will be installed by the pipeline together with the [plugins](https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html) for primateAI and spliceAI. Annotation data for CADD, spliceAI and primateAI should be downloaded. The path to the data may be specified in the corresponding [config file](config/deeprvat_annotation_config.yaml). 
+- [CADD](https://github.com/kircherlab/CADD-scripts/tree/master/src/scripts) as well as 
+- [VEP](http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html),  
+- [absplice](https://github.com/gagneurlab/absplice/tree/master), 
+- [kipoi-veff2](https://github.com/kipoi/kipoi-veff2)
+- [faatpipe](https://github.com/HealthML/faatpipe), and the
+- [vep-plugins repository](https://github.com/Ensembl/VEP_plugins/)
+
+will be installed by the pipeline together with the [plugins](https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html) for primateAI and spliceAI. Annotation data for CADD, spliceAI and primateAI should be downloaded. The path to the data may be specified in the corresponding [config file](config/deeprvat_annotation_config.yaml). 
 Download path:
 - [CADD](http://cadd.gs.washington.edu/download): "All possible SNVs of GRCh38/hg38" and "gnomad.genomes.r3.0.indel.tsv.gz" incl. their  Tabix Indices
 - [SpliceAI](https://basespace.illumina.com/s/otSPW8hnhaZR): "genome_scores_v1.3"/"spliceai_scores.raw.snv.hg38.vcf.gz" and "spliceai_scores.raw.indel.hg38.vcf.gz" 
 - [PrimateAI](https://basespace.illumina.com/s/yYGFdGih1rXL) PrimateAI supplementary data/"PrimateAI_scores_v0.2_GRCh38_sorted.tsv.bgz"
 
+
 ## Output
 
 The pipeline outputs one annotation file for VEP, CADD, DeepRiPe, DeepSea and Absplice for each input vcf-file. The tool further creates concatenated files for each tool and one merged file containing Scores from AbSplice, VEP incl. CADD, primateAI and spliceAI as well as principal components from DeepSea and DeepRiPe.