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| author | Justin Bedo <cu@cua0.org> | 2022-01-12 11:02:37 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2022-01-12 11:02:37 +1100 |
| commit | fc09e84a593aaedc1a23b17f0b1d8dda2df606df (patch) | |
| tree | 736a0241411bbf561ddf4157a2c136d57602bef1 | |
| parent | 51951403ec33c415df715d8db5ebfcd0bbebcb7f (diff) | |
gridss: add somatic variant filtering
| -rw-r--r-- | test-tnpair.nix | 1 | ||||
| -rw-r--r-- | tools/gridss.nix | 2 |
2 files changed, 3 insertions, 0 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index a08f05d..e7d5d17 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -89,6 +89,7 @@ let gridss = gridss.callVariants { } (with tnpairResult.alignments; [ normal tumour ]); gridss2 = gridss.call (with tnpairResult.alignments; [ normal tumour ]); gridss3 = gridss.callAndAssemble (with tnpairResult.alignments; [ normal tumour ]); + gridssSomatic = gridss.filterSomatic { normalName = "mysample2"; } (gridss.call (with tnpairResult.alignments; [ normal tumour ])); "merged-shards.bam" = samtools.merge { } tnpairResult.shards; "merged.bam" = samtools.merge { } [ tnpairResult.alignments.tumour tnpairResult.alignments.normal ]; "merged-namesorted.bam" = samtools.merge { } [ (nameSort tnpairResult.alignments.tumour) (nameSort tnpairResult.alignments.normal) ]; diff --git a/tools/gridss.nix b/tools/gridss.nix index f52eb6e..f5b1e0e 100644 --- a/tools/gridss.nix +++ b/tools/gridss.nix @@ -100,4 +100,6 @@ rec { # As call but include assemblies in output callAndAssemble = inputs: gridss.annotateAndAssemble { } (map gridss.preprocessBam inputs); + + filterSomatic = callBionixE ./gridss-somatic-filter.nix; } |