CNV fix

all-of-us · Nov 7, 2023 · 5a403d1 · 5a403d1
1 parent 4692f3d
commit 5a403d1
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Showing 3 changed files with 5 additions and 2 deletions.
diff --git a/docker/truvari_intrasample/pushDocker.sh b/docker/truvari_intrasample/pushDocker.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 #
-docker build --progress=plain -t fcunial/truvari_intrasample .
-docker push fcunial/truvari_intrasample
+docker build --progress=plain -t us.gcr.io/broad-dsp-lrma/aou-lr/truvari_intrasample .
+docker push us.gcr.io/broad-dsp-lrma/aou-lr/truvari_intrasample
diff --git a/docker/truvari_intrasample/resolve.py b/docker/truvari_intrasample/resolve.py
@@ -25,6 +25,8 @@ def resolve(entry, ref):
     """
     if entry.start > ref.get_reference_length(entry.chrom):
         return None
+    if entry.alts[0] in ['<CNV>', '<INS>']:
+        return None
 
     seq = ref.fetch(entry.chrom, entry.start, entry.stop)
     if entry.alts[0] == '<DEL>':

diff --git a/wdl/pipelines/TruvariIntrasample.wdl b/wdl/pipelines/TruvariIntrasample.wdl
@@ -79,6 +79,7 @@ task TruvariIntrasampleImpl {
         # - Resolves any symbolic alts (e.g. `<DEL>` with the sequence from the
         #   reference)
         #   - symbolic variants are given quality score of 1
+        # - Filters out `<CNV>` from pbsv and `<INS>` from sniffles
         # - Filters out variants greater than 100kbp (I might want to remove
         #   this)
         # - Fills in blank genotypes with `0`