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authorJustin Bedo <cu@cua0.org>2021-08-02 21:54:37 +1000
committerJustin Bedo <cu@cua0.org>2021-08-02 21:54:37 +1000
commitbc5709e934bbe1d477764fe153a198ccc669e6bb (patch)
tree87950f55f3373b8c9211c4a017437417ebb7be17 /tools
parented98174bbefc85f9895c870fdb7518e2a534a150 (diff)
gridss: drop softclip to split read conversion
Unnecessary if aligner supports split reads. Best to leave to user to manage.
Diffstat (limited to 'tools')
-rw-r--r--tools/gridss.nix3
1 files changed, 1 insertions, 2 deletions
diff --git a/tools/gridss.nix b/tools/gridss.nix
index 0e32366..6bfd495 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -60,7 +60,7 @@ rec {
/* As annotateVariants except include assembly in output */
annotateAndAssemble = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotateAndAssemble);
- /* Preprocess BAM files to extract SV reads and convert soft clips to split reads
+ /* Preprocess BAM files to extract SV reads and compute required stats
Type: preprocessBam :: bam -> bam
*/
preprocessBam = with samtools;
@@ -68,7 +68,6 @@ rec {
(gridss.extractSVReads {})
(sort {nameSort = true;})
(gridss.computeSamTags {})
- (gridss.softClipsToSplitReads {})
(sort {})
];