AlexsLemonade · kgaonkar6 · Apr 2, 2021 · Apr 6, 2021 · Apr 6, 2021 · Apr 6, 2021
diff --git a/analyses/README.md b/analyses/README.md
@@ -17,7 +17,7 @@ Note that _nearly all_ modules use the harmonized clinical data file (`pbta-hist
 | [`collapse-rnaseq`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/collapse-rnaseq) | `pbta-gene-expression-rsem-fpkm.polya.rds` <br> `pbta-gene-expression-rsem-fpkm.stranded.rds` <br> `gencode.v27.primary_assembly.annotation.gtf.gz` | Collapses RSEM FPKM matrices such that gene symbols are de-duplicated. | `results/pbta-gene-expression-rsem-fpkm-collapsed.polya.rds` (included in data download; too large for tracking via GitHub) <br> `results/pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds` (included in data download; too large for tracking via GitHub)
 | [`comparative-RNASeq-analysis`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/comparative-RNASeq-analysis) | `pbta-gene-expression-rsem-tpm.polya.rds` <br> `pbta-gene-expression-rsem-tpm.stranded.rds` <br> `pbta-histologies.tsv` <br> `pbta-mend-qc-manifest.tsv` <br> `pbta-mend-qc-results.tar.gz` | *In progress*; will produce expression outlier profiles per [#229](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/229) | N/A |
 | [`compare-gistic`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/compare-gistic) | `analyses/run-gistic/results/pbta-cnv-consensus-gistic.zip` <br> `analyses/run-gistic/results/pbta-cnv-consensus-hgat-gistic.zip` <br> `analyses/run-gistic/results/pbta-cnv-consensus-lgat-gistic.zip` <br> `analyses/run-gistic/results/pbta-cnv-consensus-medulloblastoma-gistic.zip` | Comparison of the GISTIC results of the entire cohort with the GISTIC results of three individual histolgies, namely, LGAT, HGAT and medulloblastoma ([#547](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/547) | N/A
-| [`copy_number_consensus_call`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/copy_number_consensus_call) | `pbta-cnv-cnvkit.seg.gz` <br> `pbta-cnv-controlfreec.tsv.gz` <br> `pbta-sv-manta.tsv.gz` | Produces consensus copy number calls per [#128](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/128) and a set of excluded regions where CNV calls are not made | `results/cnv_consensus.tsv` <br> `results/pbta-cnv-consensus.seg.gz` (included in data download) <br> `ref/cnv_excluded_regions.bed` <br> `ref/cnv_callable.bed`
+| [`copy_number_consensus_call`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/copy_number_consensus_call) | `pbta-cnv-cnvkit.seg.gz` <br> `pbta-cnv-controlfreec.tsv.gz` <br> `pbta-sv-manta.tsv.gz` | Produces consensus copy number calls per [#128](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/128) and a set of excluded regions where CNV calls are not made as per [#1010](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/1010) | `results/cnv_consensus.tsv` <br> `results/pbta-cnv-consensus.seg.gz` (included in data download) <br> `ref/cnv_excluded_regions.bed` <br> `ref/cnv_callable.bed`
 | [`create-subset-files`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/create-subset-files) | All files | This module contains the code to create the subset files used in continuous integration | All subset files for continuous integration
 | [`focal-cn-file-preparation`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/focal-cn-file-preparation) | `pbta-cnv-cnvkit.seg.gz` <br> `pbta-cnv-controlfreec.tsv.gz` <br> `pbta-gene-expression-rsem-fpkm-collapsed.polya.rds` <br> `pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds` <br> `analyses/copy_number_consensus_call/results/pbta-cnv-consensus.seg.gz` | Maps from copy number variant caller segments to gene identifiers; will be updated to take into account changes that affect entire cytobands, chromosome arms ([#186](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/186))| `results/cnvkit_annotated_cn_autosomes.tsv.gz` <br> `results/cnvkit_annotated_cn_x_and_y.tsv.gz` <br> `results/controlfreec_annotated_cn_autosomes.tsv.gz` <br> `results/controlfreec_annotated_cn_x_and_y.tsv.gz` <br> `results/consensus_seg_annotated_cn_autosomes.tsv.gz` (included in data download) <br> `results/consensus_seg_annotated_cn_x_and_y.tsv.gz` (included in data download)
 | [`fusion_filtering`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/fusion_filtering) | `pbta-fusion-arriba.tsv.gz` <br> `pbta-fusion-starfusion.tsv.gz` | Standardizes, filters, and prioritizes fusion calls | `results/pbta-fusion-putative-oncogenic.tsv`(included in data download) <br> `results/pbta-fusion-recurrent-fusion-byhistology.tsv` (included in data download) <br> `results/pbta-fusion-recurrent-fusion-bysample.tsv` (included in data download)

diff --git a/analyses/cnv-chrom-plot/cn_status_heatmap.nb.html b/analyses/cnv-chrom-plot/cn_status_heatmap.nb.html
diff --git a/analyses/cnv-chrom-plot/gistic_plot.nb.html b/analyses/cnv-chrom-plot/gistic_plot.nb.html
diff --git a/analyses/cnv-chrom-plot/plots/ATRT_plot.png b/analyses/cnv-chrom-plot/plots/ATRT_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Adenoma_plot.png b/analyses/cnv-chrom-plot/plots/Adenoma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Benign tumor_plot.png b/analyses/cnv-chrom-plot/plots/Benign tumor_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/CNS RMS_plot.png b/analyses/cnv-chrom-plot/plots/CNS RMS_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/CNS lymphoma_plot.png b/analyses/cnv-chrom-plot/plots/CNS lymphoma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Cavernoma_plot.png b/analyses/cnv-chrom-plot/plots/Cavernoma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Chordoma_plot.png b/analyses/cnv-chrom-plot/plots/Chordoma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Choroid plexus tumor_plot.png b/analyses/cnv-chrom-plot/plots/Choroid plexus tumor_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Craniopharyngioma_plot.png b/analyses/cnv-chrom-plot/plots/Craniopharyngioma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/DNET_plot.png b/analyses/cnv-chrom-plot/plots/DNET_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Dysplasia_plot.png b/analyses/cnv-chrom-plot/plots/Dysplasia_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/ETMR_plot.png b/analyses/cnv-chrom-plot/plots/ETMR_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/EWS_plot.png b/analyses/cnv-chrom-plot/plots/EWS_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Embryonal Tumor_plot.png b/analyses/cnv-chrom-plot/plots/Embryonal Tumor_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Embryonal tumor_plot.png b/analyses/cnv-chrom-plot/plots/Embryonal tumor_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Ependymoma_plot.png b/analyses/cnv-chrom-plot/plots/Ependymoma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Fibromyxoid lesion_plot.png b/analyses/cnv-chrom-plot/plots/Fibromyxoid lesion_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Ganglioglioma_plot.png b/analyses/cnv-chrom-plot/plots/Ganglioglioma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Germ cell tumor_plot.png b/analyses/cnv-chrom-plot/plots/Germ cell tumor_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Germinoma_plot.png b/analyses/cnv-chrom-plot/plots/Germinoma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Glial-neuronal tumor NOS_plot.png b/analyses/cnv-chrom-plot/plots/Glial-neuronal tumor NOS_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/HGAT_plot.png b/analyses/cnv-chrom-plot/plots/HGAT_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Hemangioblastoma_plot.png b/analyses/cnv-chrom-plot/plots/Hemangioblastoma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/JXG_plot.png b/analyses/cnv-chrom-plot/plots/JXG_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/LGAT_plot.png b/analyses/cnv-chrom-plot/plots/LGAT_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Langerhans Cell histiocytosis_plot.png b/analyses/cnv-chrom-plot/plots/Langerhans Cell histiocytosis_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Langerhans cell histiocytosis_plot.png b/analyses/cnv-chrom-plot/plots/Langerhans cell histiocytosis_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/MPNST_plot.png b/analyses/cnv-chrom-plot/plots/MPNST_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Medulloblastoma_plot.png b/analyses/cnv-chrom-plot/plots/Medulloblastoma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Melanocytic tumor_plot.png b/analyses/cnv-chrom-plot/plots/Melanocytic tumor_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Meningioma_plot.png b/analyses/cnv-chrom-plot/plots/Meningioma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Metastases_plot.png b/analyses/cnv-chrom-plot/plots/Metastases_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Myofibroblastoma_plot.png b/analyses/cnv-chrom-plot/plots/Myofibroblastoma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Neuroblastoma_plot.png b/analyses/cnv-chrom-plot/plots/Neuroblastoma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Neurocytoma_plot.png b/analyses/cnv-chrom-plot/plots/Neurocytoma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Neurofibroma_plot.png b/analyses/cnv-chrom-plot/plots/Neurofibroma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Oligodendroglioma_plot.png b/analyses/cnv-chrom-plot/plots/Oligodendroglioma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Other_plot.png b/analyses/cnv-chrom-plot/plots/Other_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Pineoblastoma_plot.png b/analyses/cnv-chrom-plot/plots/Pineoblastoma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Rosai-Dorfman disease_plot.png b/analyses/cnv-chrom-plot/plots/Rosai-Dorfman disease_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/SEGA_plot.png b/analyses/cnv-chrom-plot/plots/SEGA_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Sarcoma_plot.png b/analyses/cnv-chrom-plot/plots/Sarcoma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Schwannoma_plot.png b/analyses/cnv-chrom-plot/plots/Schwannoma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Teratoma_plot.png b/analyses/cnv-chrom-plot/plots/Teratoma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/Xanthogranuloma_plot.png b/analyses/cnv-chrom-plot/plots/Xanthogranuloma_plot.png
diff --git a/analyses/cnv-chrom-plot/plots/cn_status_heatmap.png b/analyses/cnv-chrom-plot/plots/cn_status_heatmap.png
diff --git a/analyses/cnv-chrom-plot/plots/gistic_plot.png b/analyses/cnv-chrom-plot/plots/gistic_plot.png
diff --git a/analyses/copy_number_consensus_call/README.md b/analyses/copy_number_consensus_call/README.md
@@ -66,10 +66,10 @@ Since there are 3 callers, there were 3 comparisons: `manta-cnvkit`, `manta-free
 14) The `results/cnv_consensus.tsv` is translated into a `results/pbta-cnv-consensus.seg` file in the same format as `pbta-cnv-cnvkit.seg.gz`, including all samples where at least two callers passed quality filtering.
 When a consensus segment is derived from multiple source segments, we take the mean of the CNVkit `seg.mean` values from the source segments, weighted by segment length.
 If no CNVkit variant was included, the value for this column is NA.
-The `copy.num` column is the weighted median of CNVkit segment values where they exist, or Control-FREEC values in the absence of CNVkit data.
+The `copy.num` column is the weighted median of Control-FREEC segment values where they exist, or CNVkit values in the absence of Control-FREEC data.
 Because some software (notably GISTIC) requires all samples to have the same regions called, the copy number variants from `cnv_consensus.tsv` are supplementented with "neutral" segments where no call was made.
 These include all non-variant regions present in `ref/cnv_callable.bed`
-The neutral regions are assigned copy.num 2, except on chrX and chrY, where the copy number is left NA.
+The neutral regions are assigned copy.num NA.
 
 ## Example Output File
 

diff --git a/analyses/copy_number_consensus_call/results/pbta-cnv-consensus.seg.gz b/analyses/copy_number_consensus_call/results/pbta-cnv-consensus.seg.gz
diff --git a/analyses/copy_number_consensus_call/run_consensus_call.sh b/analyses/copy_number_consensus_call/run_consensus_call.sh
diff --git a/analyses/copy_number_consensus_call/scripts/bed_to_segfile.R b/analyses/copy_number_consensus_call/scripts/bed_to_segfile.R
@@ -123,8 +123,8 @@ cnvs <- cnvs %>%
                 segmean = purrr::map_dbl(cnvkit_df, segmean_function),
                 cnvkit_cn = purrr::map_dbl(cnvkit_df, copies_wmedian),
                 freec_cn = purrr::map_dbl(freec_df, copies_wmedian),
-                copynum = ifelse(is.finite(cnvkit_cn), # use cnvkit if available
-                                 cnvkit_cn, freec_cn), #otherwise use freec
+                copynum = ifelse(is.finite(freec_cn), # use freec if available
+                                 freec_cn, cnvkit_cn), #otherwise use cnvkit
                 num.mark = NA)
 
 
@@ -155,7 +155,7 @@ out_neutral <- neutral %>%
                 loc.end = end) %>%
   dplyr::mutate(num.mark = NA,
                 seg.mean = NA,
-                copy.num = 2)
+                copy.num = NA)
 # unset X and Y copy numbers
 out_neutral$copy.num[out_neutral$chrom %in% c("chrX", "chrY")] <- NA
 

diff --git a/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.nb.html b/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.nb.html
diff --git a/analyses/focal-cn-file-preparation/03-add-cytoband-status-consensus.nb.html b/analyses/focal-cn-file-preparation/03-add-cytoband-status-consensus.nb.html
diff --git a/analyses/focal-cn-file-preparation/05-define-most-focal-cn-units.nb.html b/analyses/focal-cn-file-preparation/05-define-most-focal-cn-units.nb.html
diff --git a/analyses/focal-cn-file-preparation/06-find-recurrent-calls.nb.html b/analyses/focal-cn-file-preparation/06-find-recurrent-calls.nb.html
diff --git a/analyses/focal-cn-file-preparation/plots/all_histology_cn_counts.png b/analyses/focal-cn-file-preparation/plots/all_histology_cn_counts.png
diff --git a/...-preparation/plots/consensus_seg_annotated_cn_autosomes_polya_loss_cor_plot.png b/...-preparation/plots/consensus_seg_annotated_cn_autosomes_polya_loss_cor_plot.png
diff --git a/...e-preparation/plots/consensus_seg_annotated_cn_autosomes_polya_stacked_plot.png b/...e-preparation/plots/consensus_seg_annotated_cn_autosomes_polya_stacked_plot.png
diff --git a/...-preparation/plots/consensus_seg_annotated_cn_autosomes_polya_zero_cor_plot.png b/...-preparation/plots/consensus_seg_annotated_cn_autosomes_polya_zero_cor_plot.png
diff --git a/...eparation/plots/consensus_seg_annotated_cn_autosomes_stranded_loss_cor_plot.png b/...eparation/plots/consensus_seg_annotated_cn_autosomes_stranded_loss_cor_plot.png
diff --git a/...reparation/plots/consensus_seg_annotated_cn_autosomes_stranded_stacked_plot.png b/...reparation/plots/consensus_seg_annotated_cn_autosomes_stranded_stacked_plot.png
diff --git a/...eparation/plots/consensus_seg_annotated_cn_autosomes_stranded_zero_cor_plot.png b/...eparation/plots/consensus_seg_annotated_cn_autosomes_stranded_zero_cor_plot.png
diff --git a/...le-preparation/plots/consensus_seg_annotated_cn_x_and_y_polya_loss_cor_plot.png b/...le-preparation/plots/consensus_seg_annotated_cn_x_and_y_polya_loss_cor_plot.png
diff --git a/...ile-preparation/plots/consensus_seg_annotated_cn_x_and_y_polya_stacked_plot.png b/...ile-preparation/plots/consensus_seg_annotated_cn_x_and_y_polya_stacked_plot.png
diff --git a/...le-preparation/plots/consensus_seg_annotated_cn_x_and_y_polya_zero_cor_plot.png b/...le-preparation/plots/consensus_seg_annotated_cn_x_and_y_polya_zero_cor_plot.png
diff --git a/...preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_loss_cor_plot.png b/...preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_loss_cor_plot.png
diff --git a/...-preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_stacked_plot.png b/...-preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_stacked_plot.png
diff --git a/...preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_zero_cor_plot.png b/...preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_zero_cor_plot.png
diff --git a/analyses/focal-cn-file-preparation/plots/separate_histology_cn_counts.png b/analyses/focal-cn-file-preparation/plots/separate_histology_cn_counts.png
diff --git a/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_autosomes.tsv.gz b/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_autosomes.tsv.gz
diff --git a/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_x_and_y.tsv.gz b/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_x_and_y.tsv.gz
diff --git a/analyses/focal-cn-file-preparation/results/consensus_seg_focal_cn_recurrent_genes.tsv b/analyses/focal-cn-file-preparation/results/consensus_seg_focal_cn_recurrent_genes.tsv
@@ -1,23 +1,24 @@
 gene
-BANCR
-C22orf39
-CDC45
-CLDN5
-FAM122A
-FXN
-GNB1L
-HIRA
-LINC01506
-MIR130B
-MIR301B
-PGM5
-PIEZO2
-PIP5K1B
-PPIL2
-PRKACG
-TJP2
-TMEM252
-TMEM252-DT
-UBE2L3
-UFD1
-YPEL1
+PARP12
+TBXAS1
+TTC26
+UBN2
+ZC3HAV1
+ADCK2
+BRAF
+CLEC2L
+DENND2A
+FMC1
+FMC1-LUC7L2
+HIPK2
+KDM7A
+KDM7A-DT
+KIAA1549
+KLRG2
+LUC7L2
+MKRN1
+NDUFB2
+NDUFB2-AS1
+RAB19
+SLC37A3
+ZC3HAV1L
diff --git a/analyses/focal-cn-file-preparation/results/consensus_seg_most_focal_cn_status.tsv.gz b/analyses/focal-cn-file-preparation/results/consensus_seg_most_focal_cn_status.tsv.gz