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| author | Justin Bedo <cu@cua0.org> | 2019-04-08 09:33:33 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-04-08 09:33:33 +1000 |
| commit | 001e834a4b8e660be8797690a2b0eb418b01fbbb (patch) | |
| tree | 4201553068072c62f5f7deb6e155d7c721d3a0b5 /test-tnpair.nix | |
| parent | 51dbff37cc69737c47cd4c2c758bb252054497ad (diff) | |
grids: add function to include assemblies with annotated VCF
Diffstat (limited to 'test-tnpair.nix')
| -rw-r--r-- | test-tnpair.nix | 1 |
1 files changed, 1 insertions, 0 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index da37068..c88b68a 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -51,6 +51,7 @@ let (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") + (ln (gridss.callAndAssemble (with tnpairResult.alignments; [normal tumour])) "gridss3") (ln (samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal]) "alignments/merged.bam") (ln (samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour)) "alignments/${tnpair.tumour.name}.cram") #(ln (samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.normal)) "alignments/${tnpair.normal.name}.cram") |