diff options
| author | Justin Bedo <cu@cua0.org> | 2019-01-15 14:31:15 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-01-15 14:31:15 +1100 |
| commit | 2bf74101a862d0417ccda2bafe55e0d2616d1e1a (patch) | |
| tree | 159d71089e2057f711bf756e18fdea9a494b3825 /test-tnpair.nix | |
| parent | ddd1c7549995600ab32c5b7a9112334681d3ea8a (diff) | |
strelka: add germline calling
Diffstat (limited to 'test-tnpair.nix')
| -rw-r--r-- | test-tnpair.nix | 4 |
1 files changed, 3 insertions, 1 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index c531a83..8b268ec 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -15,7 +15,7 @@ let sort = samtools.sort {}; flagstat = samtools.flagstat {}; check = fastqc.check {}; - callVariants = strelka.call {}; + callVariants = strelka.callSomatic {}; markdup = samtools.markdup {}; fixmate = samtools.fixmate {}; @@ -35,6 +35,7 @@ let processPair = { tumour, normal }: rec { alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG x.name x.files)))) { inherit normal tumour; }; variants = callVariants alignments; + glvariants = strelka.call {} (builtins.attrValues alignments); platypusVars = platypus.call {} (builtins.attrValues alignments); }; @@ -43,6 +44,7 @@ let testNaming = linkDrv [ (ln (facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];}) "facets") (ln tnpairResult.variants "strelka") + (ln tnpairResult.glvariants "strelka-gl") (ln (bowtie.align {inherit ref;} tnpair.normal.files) "alignments/bowtie-normal.bam") (ln (gridss.callVariants {} (with tnpairResult.alignments; [normal tumour])) "gridss") (ln (gridss.call (with tnpairResult.alignments; [normal tumour])) "gridss2") |