Merge pull request #85 from tlesluyes/master

Prepapre for v2.5.3

README.md

@@ -9,11 +9,6 @@ ASCAT is described in detail in: [Allele-specific copy number analysis of tumors
 This repository also contains the code underlying additional publication:
 [Allele-specific multi-sample copy number segmentation. Ross EM, Haase K, Van Loo P & Markowetz F. *Bioinformatics* (2020)](https://pubmed.ncbi.nlm.nih.gov/32449758).
 
-## Future v3 release (beta-test version)
-We are pleased to announce that an early version of the future v3 release is available here: [https://github.com/VanLoo-lab/ascat/tree/v3.0](https://github.com/VanLoo-lab/ascat/tree/v3.0).
-
-This beta version comes with major improvements and new features. Therefore, we recommend users to give it a try, as early adopters, before it becomes the latest (and default) version of ASCAT.
-
 ## Installation
 `devtools::install_github('VanLoo-lab/ascat/ASCAT')`
 

ReleasedData/TCGA_SNP6_hg19/README.md

@@ -4,3 +4,6 @@
   > TCGA-04-1351, TCGA-04-1371, TCGA-06-0178, TCGA-57-1586, TCGA-V5-AASX-b
 #### Set pass=FALSE for the following 53 samples because of large CNVs (>10Mb) in germlines:
   > TCGA-05-4403, TCGA-06-2559, TCGA-12-3651, TCGA-25-1877, TCGA-26-5135, TCGA-2G-AAEW, TCGA-77-6842-a, TCGA-86-8054, TCGA-91-A4BD, TCGA-97-8179, TCGA-A5-A2K4, TCGA-A8-A07L, TCGA-AB-2812, TCGA-AB-2843, TCGA-AB-2847, TCGA-AB-2855, TCGA-AB-2856, TCGA-AB-2887, TCGA-AB-2891, TCGA-AB-2909, TCGA-AB-2913, TCGA-AB-2924, TCGA-AB-2944, TCGA-AB-2954, TCGA-AB-2997, TCGA-AB-3008, TCGA-AC-A2QJ, TCGA-AH-6547, TCGA-AP-A0LQ, TCGA-AY-4071, TCGA-BH-A1EW, TCGA-BJ-A28W-a, TCGA-BK-A139-e, TCGA-BM-6198, TCGA-BT-A20U, TCGA-C5-A1MK, TCGA-CG-5717, TCGA-CH-5753, TCGA-CH-5769, TCGA-CV-6441, TCGA-D8-A146, TCGA-D8-A1XC, TCGA-DD-AAEH, TCGA-DJ-A2Q2, TCGA-DM-A1D6, TCGA-E2-A15G, TCGA-EE-A29D, TCGA-EY-A1G8, TCGA-FD-A62N, TCGA-FS-A4F0, TCGA-GS-A9U4, TCGA-P5-A72U, TCGA-UZ-A9PJ
+
+## Update 2
+**A newer and improved data release is available as part of ASCAT v3. Therefore, this dataset should not be used any longer. We fixed an issue where CNAs were not correctly reported in chrX for males, as there were inconsistent signals between logR and BAF in this dataset. This has been resolved in ASCAT v3.**