diff --git a/analyses/genomicData/MAFinBED.R b/analyses/genomicData/MAFinBED.R index f7aea23d..6077ced9 100644 --- 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 index d1baab13..ee35d429 100644 --- 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 index fa2d6b44..d2d1aff1 100644 --- 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 index bf95e842..e4cf72a1 100644 --- 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',