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authorJustin Bedo <cu@cua0.org>2019-06-20 08:22:32 +1000
committerJustin Bedo <cu@cua0.org>2019-06-21 10:42:26 +1000
commit7231886ee52379de001ae830ed76a09be556ac57 (patch)
treeb0d75c136a170449e077cf07d1fb5e555b4a0c0f
parentff8a11320db7131e488423e103937a342b82e652 (diff)
Add CNVkit test
-rw-r--r--test-tnpair.nix7
1 files changed, 7 insertions, 0 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix
index 4d6a794..0e13338 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -47,8 +47,15 @@ let
tnpairResult = processPair tnpair;
+ cnvkitResults = rec {
+ cnvs = cnvkit.callCNV {} (with tnpairResult.alignments; { normals = [ normal ]; tumours = [ tumour ];});
+ plot = cnvkit.scatterPlot {} cnvs;
+ };
+
testNaming = linkDrv [
(ln (facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];}) "facets")
+ (ln cnvkitResults.cnvs "cnvkit")
+ (ln cnvkitResults.plot "cnvkit.pdf")
(ln tnpairResult.variants "strelka")
(ln tnpairResult.glvariants "strelka-gl")
(ln tnpairResult.variants.indels "strelka.indels.vcf")