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| author | Justin Bedo <cu@cua0.org> | 2019-06-19 11:24:38 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-07-03 14:59:27 +1000 |
| commit | 0b6b3fa8fc20461b41a368b82c62c2f9d7472b31 (patch) | |
| tree | 5c0e9aaf7fce678f1b930c3d27bfafb88ffc7a27 /test-tnpair.nix | |
| parent | 999743ce240460dc25b29ed1a4db0989fd3e955c (diff) | |
octopus: initial functions
Diffstat (limited to 'test-tnpair.nix')
| -rw-r--r-- | test-tnpair.nix | 4 |
1 files changed, 4 insertions, 0 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index 76fcfab..f90e3a9 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -37,8 +37,10 @@ let processPair = { tumour, normal }: rec { alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG x.name x.files)))) { inherit normal tumour; }; variants = callVariants alignments; + octopusSomatic = octopus.callSomatic {} {inherit (alignments) normal; tumours = [ alignments.tumour ];}; glvariants = strelka.call {} (builtins.attrValues alignments); platypusVars = platypus.call {} (builtins.attrValues alignments); + octopusVars = octopus.call {} (builtins.attrValues alignments); shards = pipe [ (shard.fastQPair 2) (map (bwa.align {inherit ref;})) @@ -56,6 +58,8 @@ let (ln (facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];}) "facets") (ln cnvkitResults.cnvs "cnvkit") (ln cnvkitResults.plot "cnvkit.pdf") + (ln tnpairResult.octopusVars "octopus.vcf") + (ln tnpairResult.octopusSomatic "octopus-somatic.vcf") (ln tnpairResult.variants "strelka") (ln tnpairResult.glvariants "strelka-gl") (ln tnpairResult.variants.indels "strelka.indels.vcf") |