From 0ade062d2da8a7111b14aa3d72ef7c741e98352d Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Thu, 22 Nov 2018 10:44:31 +1100 Subject: gridss: restructure gridss pipeline --- tools/gridss.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'tools/gridss.nix') diff --git a/tools/gridss.nix b/tools/gridss.nix index 1e4e2d1..b85e84e 100644 --- a/tools/gridss.nix +++ b/tools/gridss.nix @@ -17,6 +17,6 @@ rec { assemble = callBionix ./gridss-assemble.nix; identifyVariants = callBionix ./gridss-identifyVariants.nix; annotateVariants = callBionix ./gridss-annotateVariants.nix; - preprocessBam = input: with samtools; markdup {} (sort {} (fixmate {mateScore = true;} (bionix.gridss.softClipsToSplitReads {} (bionix.gridss.computeSamTags {} (sort {nameSort = true;} input))))); - call = inputs: bionix.gridss.annotateVariants {} (map bionix.gridss.preprocessBam inputs); + preprocessBam = input: with samtools; sort {} (gridss.softClipsToSplitReads {} (gridss.computeSamTags {} (sort {nameSort = true;} (gridss.extractSVReads {} (markdup {} (sort {} (fixmate {mateScore = true;} (sort {nameSort = true;} input)))))))); + call = inputs: bionix.gridss.annotateVariants {} (map gridss.preprocessBam inputs); } -- cgit v1.2.3