From 989a8930f7a2b2b25150aa78483db24972efaae9 Mon Sep 17 00:00:00 2001 From: dantaki Date: Thu, 22 Jun 2017 19:26:41 -0700 Subject: [PATCH] sv2 v1.3 with -M option for legacy bwa mem -M BAM files: split-reads are flagged as secondary instead of supplementary --- doc/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/README.md b/doc/README.md index ea5d34a..922d5c7 100644 --- a/doc/README.md +++ b/doc/README.md @@ -388,7 +388,7 @@ sv2 -i HG00096_sv2_input.txt -r chr21_forestSV.bed -M -o HG00096_sv2 sv2 -i HG01051_sv2_input.txt -r chr21_forestSV.bed -M -o HG01051_sv2 ``` -**Note**: since the BAM files were generated with the legacy `-M` option that flags split-reads as secondary, supply the `-M` flag to SV2 +**Note**: since the BAM files were algined with bwa mem with the legacy `-M` option that flags split-reads as secondary, supply the `-M` flag to SV2 ##### Run SV2 for multiple samples