From 3acfec672179b41bc645fb00f293ce3ae3847dc1 Mon Sep 17 00:00:00 2001 From: Azhar Khandekar Date: Sat, 14 Dec 2024 11:31:21 -0500 Subject: [PATCH] Update README.md Added link to README to clarify BRASS convention for SVs --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index dd6c9db..d07d68b 100755 --- a/README.md +++ b/README.md @@ -101,7 +101,7 @@ a DBS, SBS, ID, and TSB folder (there will also be a plots folder if this parame ### INPUT FORMAT: -***First six columns are required, and either the column "svclass" (deletion, translocation, tandem-duplication, or inversion) or the columns "strand1" & "strand2" (BRASS convention) must also be present*** +***First six columns are required, and either the column "svclass" (deletion, translocation, tandem-duplication, or inversion) or the columns "strand1" & "strand2" (BRASS convention, see https://github.com/cancerit/BRASS/wiki/BEDPE) must also be present*** ### Example with SV class present (tsv or csv file): @@ -249,12 +249,12 @@ python3 test.py -t GRCh37 **CITATION** -For SBSs, DBSs, and INDELs, please cite the following paper: +**For SBSs, DBSs, and INDELs, please cite the following paper:** Bergstrom EN, Huang MN, Mahto U, Barnes M, Stratton MR, Rozen SG, and Alexandrov LB (2019) SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events. **BMC Genomics** 20, Article number: 685. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6041-2 -For SVs and CNVs, please cite the following paper: +**For SVs and CNVs, please cite the following paper:** Khandekar A, Vangara R, Barnes M, Díaz-Gay M, Abbasi A, Bergstrom EN, Steele CD, Pillay N, and Alexandrov LB (2023) Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator. **BMC Genomics** 24, Article number: 469. https://doi.org/10.1186/s12864-023-09584-y