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| author | l-d-s <distefano.l@wehi.edu.au> | 2018-11-22 12:04:23 +1100 |
|---|---|---|
| committer | l-d-s <distefano.l@wehi.edu.au> | 2018-11-22 12:04:23 +1100 |
| commit | 7c36ee4ec628767c834ad803aac76d93e31f0486 (patch) | |
| tree | 2edf423614fc077c4027b7996f690b004ec4f25b /tools/gridss.nix | |
| parent | 3c568bacd397a3ddcb203811f7fa5a1f8af760a3 (diff) | |
| parent | 0ade062d2da8a7111b14aa3d72ef7c741e98352d (diff) | |
Merge branch 'master' of https://github.com/PapenfussLab/bionix
Diffstat (limited to 'tools/gridss.nix')
| -rw-r--r-- | tools/gridss.nix | 4 |
1 files changed, 2 insertions, 2 deletions
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); } |