Fix maf in bed filter (#344)

* Remove lines * Update setup * Don't reference alt * Add note about release notes
Sage-Bionetworks · Aug 5, 2020 · 5dfa14c · 5dfa14c
1 parent 5a83a7c
commit 5dfa14c
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Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/analyses/genomicData/MAFinBED.R b/analyses/genomicData/MAFinBED.R
@@ -122,9 +122,9 @@ mafVR = VRanges(seqnames = Rle(paste0("chr",genieMutData$Chromosome)),
                 ranges = IRanges(start = genieMutData$Start_Position,
                                  end = genieMutData$End_Position),
                 ref = genieMutData$Reference_Allele,
-                alt = genieMutData$Tumor_Seq_Allele2,
+                # alt = genieMutData$Tumor_Seq_Allele2,
                 altDepth = genieMutData$t_alt_count_num,
-                totalDepth = genieMutData$t_depth_new,
+                # totalDepth = genieMutData$t_depth_new,
                 sampleNames = genieMutData$Tumor_Sample_Barcode)
 seqlevels(mafVR) = sort(seqlevels(mafVR))
 

diff --git a/analyses/mergeFlag/mergecheck_functions.R b/analyses/mergeFlag/mergecheck_functions.R
@@ -99,7 +99,7 @@ flag_variants_to_merge <- function(genieMutData, genieClinData, samplesToRun, up
                   ranges = IRanges(start = genieMutData$Start_Position,
                                    end = genieMutData$End_Position),
                   ref = genieMutData$Reference_Allele,
-                  alt = genieMutData$Tumor_Seq_Allele2,
+                  # alt = genieMutData$Tumor_Seq_Allele2,
                   altDepth = genieMutData$t_alt_count_num,
                   totalDepth = genieMutData$t_depth,
                   sampleNames = genieMutData$Tumor_Sample_Barcode)

diff --git a/genie/dashboardTemplate.Rmd b/genie/dashboardTemplate.Rmd
@@ -578,7 +578,7 @@ kable(final_matrix,
 
 ### Panels Covering TP53
 
-These are all the pipelines that cover TP53 that don't have TP53 as the top mutated genes.  If your pipeline is shown in the table below, it is _possible_ that you have artifacts in your data.  **Please review and reupload if your data is incorrect**
+These are all the pipelines that cover TP53 that don't have TP53 as the top mutated genes.  If your pipeline is shown in the table below, it is _possible_ that you have artifacts in your data.  **Please review and reupload if your data is incorrect**  The release notes will capture if sites have confirmed that the variants shown in this table has no artifacts.
 
 
 ```{r highlight_panels, echo=FALSE}

diff --git a/setup.py b/setup.py
@@ -27,7 +27,7 @@
       entry_points={'console_scripts': ['genie = genie.__main__:main']},
       scripts=['bin/input_to_database.py',
                'bin/database_to_staging.py'],
-      install_requires=['pandas>=0.23.0',
+      install_requires=['pandas>=0.23.0,<1.1',
                         'synapseclient>=1.9.4',
                         'httplib2>=0.11.3',
                         'pycrypto>=2.6.1',