Merge branch 'beta_test' into HEAD

.gitmodules

@@ -16,3 +16,9 @@
 [submodule "tools/cnvkit"]
 	path = tools/cnvkit
 	url = https://github.com/etal/cnvkit.git
+[submodule "tools/msisensor2"]
+	path = tools/msisensor2
+	url = https://github.com/niu-lab/msisensor2.git
+[submodule "tools/msisensor-pro"]
+	path = tools/msisensor-pro
+	url = https://github.com/xjtu-omics/msisensor-pro

CHANGELOG.md

@@ -1,5 +1,14 @@
 # Changelog
 
+## Release v4.0.0
+
+* Integration of Mutect2 (GATK4) for tumorOnly and Panel variant calling
+* Analysis of the TSO500 panel handels of the DNA and RNA part of the panel
+* Calcualtion of various complex biomarkers like TMB, MSI, HRD,
+* Calcualtion of more QC metrics, e.g. bioinformatic tumor cell content (purity)
+* Various bugfixes
+* Adjustments of the PDF report mainly structure and readability
+
 ## Release v3.1.0
 
 * Updated ClinVar version to clinvar_20210123; re-run of ./setup.sh -t setup_tools from the MIRACUM-Pipe-docker repository recommended or manual installation of the updated annovar databases:

RScripts/HRD.R

@@ -0,0 +1,25 @@
+library(scarHRD)
+library(sequenza)
+
+args <- commandArgs()
+ID <- args[6]
+path <- args[7]
+
+print(args)
+print(ID)
+print(path)
+setwd(path)
+getwd()
+
+input_file <- paste0(path, "/", ID, ".small.seqz.gz")
+print(input_file)
+# Determine the HRD-Score
+result <- scar_score(input_file, reference = "grch37", seqz = TRUE)
+write.table(x = result, file = paste0(path, "/", ID, "_HRD.txt"))
+# CNV analysis of SEQUENZA to determine tumor purity and ploidy
+extr <- sequenza.extract(input_file, verbose = FALSE)
+cp <- sequenza.fit(extr)
+sequenza.results(
+    sequenza.extract = extr, cp.table = cp, sample.id = ID,
+    out.dir = paste0(path, "/", ID, "_sequenza")
+)