diff options
| author | Justin Bedo <cu@cua0.org> | 2019-06-20 08:22:32 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-06-21 10:42:26 +1000 |
| commit | 7231886ee52379de001ae830ed76a09be556ac57 (patch) | |
| tree | b0d75c136a170449e077cf07d1fb5e555b4a0c0f /test-tnpair.nix | |
| parent | ff8a11320db7131e488423e103937a342b82e652 (diff) | |
Add CNVkit test
Diffstat (limited to 'test-tnpair.nix')
| -rw-r--r-- | test-tnpair.nix | 7 |
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") |