Merge branch 'master' of https://github.com/ding-lab/CPTAC3.catalog

AdamDanielHarris · Nov 4, 2022 · 6a73a15 · 6a73a15
2 parents 5749042 + ebd1f38
commit 6a73a15
Show file tree

Hide file tree

Showing 6 changed files with 29 additions and 5,130 deletions.
diff --git a/DCC_Analysis_Summary/README.Y3.md b/DCC_Analysis_Summary/README.Y3.md
@@ -1,12 +1,12 @@
 
-Last updated: 9/20/21
+Last updated: 9/22/22
 
 **BOLD** are new since 5/18/22
 
 ## Analysis Summaries - Case counts - Y3 only
 Pipeline                        | AML | CCRCC | CM  | GBM | HNSCC | LSCC | LUAD | PDA | SAR | UCEC | Total
 ---                             | --- | ----- | --- | --- | ----- | ---- | ---- | --- | --- | ---- | ---
-Methylation Array               | 115  | 260   | 8   | 205 | 111   | 202  | 229  | 164 | 19  | 249  | 1562
+Methylation Array               |**172**| 260   | 8 |**239**| 111   | 202  | 229  | 164 | 19  | 249  |**1653**
 miRNA-Seq                       |**172**|82   | 3   |**249**| 22  |  104 |  72  | 164 |  0  |  35  | **903**
 RNA-Seq Expression              |**172**|261  | 8   |**243**| 111   |  202 | 229  | 186 | 19  | 252  |**1683**
 RNA-Seq Fusion                  |**172**| 110   | 0 |**127**| 0     |  89  | 109  | 81  |  0  | 170  | **858**
@@ -23,7 +23,7 @@ WXS Germline                    |**160**| 259   | 0 |**230**|  111  |  199 |229|
 
 Pipeline                        | AML | CCRCC | CM  | GBM | HNSCC | LSCC | LUAD | PDA | SAR | UCEC | Total
 ---                             | --- | ----- | --- | --- | ----- | ---- | ---- | --- | --- | ---- | ---
-Methylation Array               | 115 | 260   | 8   | 205 | 111   | 202  | 229  | 164 | 19  | 249  | 1562
+Methylation Array               | 172 | 260   | 8   | 239 | 111   | 202  | 229  | 164 | 19  | 249  | 1653
 miRNA-Seq                       | 172 | 261   | 8   | 249 | 111   | 202  | 229  | 164 | 19  | 250  | 1665
 RNA-Seq Expression              | 172 | 261   | 8   | 243 | 111   | 202  | 229  | 186 | 19  | 252  | 1683
 RNA-Seq Fusion                  | 172 | 222   | 8   | 243 | 111   | 202  | 229  | 164 | 19  | 246  | 1616

diff --git a/DCC_Analysis_Summary/README.md b/DCC_Analysis_Summary/README.md
@@ -19,40 +19,34 @@ DCC Analysis Summary files have the following initial columns:
 10. md5sum
 ```
 
-NEW: Column C3Y indicates "CPTAC3 Year" and takes values `Y1`, `Y2`, etc.  It is used for administrative purposes.
+Column C3Y indicates "CPTAC3 Year" and takes values `Y1`, `Y2`, etc.  It is used for administrative purposes.
+
+`DCC_path` is the path of each result at the [CPTAC DCC](https://cptac-data-portal.georgetown.edu/cptac/dataPrivate/list?scope=private).
+Such results are also available relative to the following path on WUSTL RIS storage1:
+```
+/storage1/fs1/dinglab/Active/Projects/CPTAC3/Common/CPTAC3-DCC-Staging/DCC_STAGE_ROOT
+```
 
 Additional columns are specific to individual pipelines and will typically indicate the input data associated with this analysis.
 Pipelines which generate multiple result files per case will have multiple entries in the analysis summary file.
 
 ## Analysis Summaries
 
-Counts of cases processed per disease and pipeline.  Counts of results to reference other than GDC hg38 excluded.
+Counts of unique cases processed per disease and pipeline.  Last updated 9/21/22.
 
-Pipeline (last updated 10/28/21)| AML | CCRCC | CM  | GBM | HNSCC | LSCC | LUAD | PDA | SAR | UCEC | Total
+Pipeline                        | AML | CCRCC | CM  | GBM | HNSCC | LSCC | LUAD | PDA | SAR | UCEC | Total
 ---                             | --- | ----- | --- | --- | ----- | ---- | ---- | --- | --- | ---- | ---
-Methylation Array               | 43  | 260   | 8   | 205 | 111   | 202  | 229  | 164 | 19  | 249  | 1490
-miRNA-Seq                       | 42  | 261   | 8   | 184 | 111   | 202  | 229  | 164 | 19  | 250  | 1480 
-RNA-Seq Expression              | 42  | 261   | 8   | 189 | 111   | 202  | 229  | 186 | 19  | 252  | 1499 
-RNA-Seq Fusion                  | 11  | 222   | 8   | 188 | 111   | 202  | 229  | 164 | 19  | 246  | 1400 
-RNA-Seq Transcript + Splicing   | 1   | 261   | 3   | 234 | 111   | 202  | 218  | 186 | 0   | 246  | 1462
-WGS CNV Somatic                 |  0  | 258   | 0   | 187 | 111   | 202  | 229  | 166 | 0   | 243  | 1396 
-WGS SV                          | 0   | 258   | 0   | 187 | 111   | 201  | 219  | 166 | 0   | 243  | 1476 
-WXS MSI                         | 0   | 259   | 0   | 188 | 111   | 202  | 219  | 166 | 0   | 247  | 1392 
-WXS Somatic TD                  | 0   | 259   | 0   | 185 | 111   | 202  | 218  | 181 | 0   | 233  | 1401
-WXS Somatic SW                  | 0   | 260   | 0   | 185 | 111   | 202  | 218  | 181 | 0   | 247  | 1404
-WXS Germline                    | 0   | 259   | 0   | 186 | 111   | 199  | 219  | 166 | 0   | 233  | 1373
-
-
-<!--
-### QC Pipelines
-
-QC Pipelines                    | AML | CCRCC | CM  | GBM | HNSCC | LSCC | LUAD | PDA | SAR | UCEC | Total
----                             | --- | ----- | --- | --- | ----- | ---- | ---- | --- | --- | ---- | ---
-miRNA-Seq QC                    | 11  | 28    | 5   | 52  | 17    | 27   | 10   | 77  | 19  | 39   | 285 
-RNA-Seq QC                      | 11  | 112   | 8   | 119 | 111   | 113  | 53   | 83  | 19  | 77   | 706 
-WGS QC                          | 0   | 0     | 0   | 60  | 21    | 113  | 0    | 77  | 0   | 39   | 310
-WXS QC                          | 5   | 87    | 4   | 118 | 111   | 113  | 101  | 44  | 9   | 51   | 643
--->
+Methylation Array               | 172 | 260   | 8   | 239 | 111   | 202  | 229  | 164 | 19  | 249  | 1653
+miRNA-Seq                       | 172 | 261   | 8   | 249 | 111   | 202  | 229  | 164 | 19  | 250  | 1665
+RNA-Seq Expression              | 172 | 261   | 8   | 243 | 111   | 202  | 229  | 186 | 19  | 252  | 1683
+RNA-Seq Fusion                  | 172 | 222   | 8   | 243 | 111   | 202  | 229  | 164 | 19  | 246  | 1616
+RNA-Seq Transcript + Splicing   | 172 | 261   | 3   | 244 | 111   | 202  | 218  | 186 | 0   | 246  | 1643
+WGS CNV Somatic                 | 133 | 258   | 0   | 218 | 111   | 202  | 229  | 166 | 0   | 243  | 1560
+WGS SV                          | 139 | 258   | 0   | 218 | 111   | 201  | 219  | 166 | 0   | 243  | 1646 
+WXS MSI                         | 160 | 259   | 0   | 228 | 111   | 202  | 219  | 166 | 0   | 247  | 1543
+WXS Somatic TD                  | 160 | 259   | 0   | 225 | 111   | 202  | 218  | 181 | 0   | 233  | 1601
+WXS Somatic SW                  | 160 | 260   | 0   | 225 | 111   | 202  | 218  | 181 | 0   | 247  | 1604
+WXS Germline                    | 160 | 259   | 0   | 230 | 111   | 199  | 229  | 166 | 0   | 233  | 1587
 
 ## Year 1
 
@@ -71,8 +65,7 @@ pipeline details are included in documentation included with data files on DCC.
 
 ## Methylation_Array
 
-Methylation array analysis has been performed for all cases available on DCC
-through December 2019, details in
+Details in
 [`Methylation_Array.DCC_analysis_summary.dat`](Methylation_Array.DCC_analysis_summary.dat)
 
 [CPTAC3 Methylation pipeline details](https://github.com/ding-lab/cptac_methylation)
@@ -86,26 +79,16 @@ Note that each sample has results for mature miRNA, precursor miRNA, and total m
 
 [miRNA-Seq pipeline documentation](https://github.com/ding-lab/CPTAC_miRNA) and [processing description](processing_description/miRNA-Seq.processing_description.md).
 
-### miRNA-Seq QC
-
-Analysis details [`miRNA-Seq_QC.DCC_analysis_summary.dat`](miRNA-Seq_QC.DCC_analysis_summary.dat) 
-
-[QC pipeline documentation](https://github.com/ding-lab/CPTAC3_QC)
-
 ## RNA-Seq
 
 ### RNA-Seq Expression
 
-965 cases (consisting of all Y1 and Y2 cases) been analyzed
-
 Analysis details [`RNA-Seq_Expression.DCC_analysis_summary.dat`](RNA-Seq_Expression.DCC_analysis_summary.dat)
 
 [CPTAC3 RNA-Seq Expression pipeline](https://github.com/ding-lab/cptac_rna_expression)
 
 ### RNA-Seq Fusion
 
-1259 samples across 817 cases analyzed, including all of Y2 cases and LUAD from Y1.  
-
 Analysis details [`RNA-Seq_Fusion.DCC_analysis_summary.dat`](RNA-Seq_Fusion.DCC_analysis_summary.dat), and 
 [pipeline documentation on GitHub](https://github.com/cuidaniel/Fusion_hg38)
 
@@ -115,20 +98,10 @@ Analysis details [`RNA-Seq_Transcript.DCC_analysis_summary.dat`](RNA-Seq_Transcr
 
 [Pipeline documentation on GitHub](https://github.com/ding-lab/CPTAC3_splicing)
 
-### RNA-Seq QC
-
-Analysis details [`RNA-Seq_QC.DCC_analysis_summary.dat`](RNA-Seq_QC.DCC_analysis_summary.dat)
-
-[QC pipeline documentation](https://github.com/ding-lab/CPTAC3_QC)
-
-
 ## WGS
 
 ### WGS SV
 
-Year 1 LUAD analyses are included.  
-Also in the DCC analysis summary file are 109 HNSCC cases aligned to a custom reference (`GRCh38_full_analysis_set_plus_decoy_hla`) for UMich group
-
 Analysis details [`WGS_SV.DCC_analysis_summary.dat`](WGS_SV.DCC_analysis_summary.dat)
 
 [CPTAC3 SomaticSV pipeline on GitHub](https://github.com/ding-lab/somatic_sv_workflow)
@@ -139,14 +112,6 @@ Analysis details [`WGS_CNV_Somatic.DCC_analysis_summary.dat`](WGS_CNV_Somatic.DC
 
 [WGS CNV pipeline](https://github.com/ding-lab/BICSEQ2)
 
-All Y1 analyses with pipeline version v2.0 have been added to the analysis summary.
-
-### WGS QC
-
-Analysis details [`WGS_QC.DCC_analysis_summary.dat`](WGS_QC.DCC_analysis_summary.dat)
-
-[CPTAC3 QC pipeline](https://github.com/ding-lab/CPTAC3_QC)
-
 ## WXS
 
 ### WXS MSI
@@ -161,25 +126,15 @@ Analysis details [`WXS_Normal_Adjacent.DCC_analysis_summary.dat`](WXS_Normal_Adj
 
 WXS Normal Adjacent analysis generated using [TinDaisy pipeline](https://github.com/ding-lab/TinDaisy)
 
-### WXS QC
-
-Analysis details [`WXS_QC.DCC_analysis_summary.dat`](WXS_QC.DCC_analysis_summary.dat)
-
-[CPTAC3 QC pipeline](https://github.com/ding-lab/CPTAC3_QC)
-
-### WXS Somatic
+### WXS Somatic TD
 
-WXS Somatic analysis is new for CPTAC3 Year 3.  So far only 113 LSCC cases have been analyzed using 
-[TinDaisy variant caller v2.1](https://github.com/ding-lab/TinDaisy)
+WXS Somatic analysis [TinDaisy variant caller v2.1](https://github.com/ding-lab/TinDaisy)
 
-Analysis details [`WXS_Somatic.DCC_analysis_summary.dat`](WXS_Somatic.DCC_analysis_summary.dat)
+Analysis details [`WXS_Somatic_Variant_TD.DCC_analysis_summary.dat`](WXS_Somatic_Variant_TD.DCC_analysis_summary.dat"
 
 ### WXS Somatic SW
 
-113 LSCC and 109 LUAD cases in [`WXS_Somatic_Variant_SW.DCC_analysis_summary.dat`](WXS_Somatic_Variant_SW.DCC_analysis_summary.dat).  
+[`WXS_Somatic_Variant_SW.DCC_analysis_summary.dat`](WXS_Somatic_Variant_SW.DCC_analysis_summary.dat).  
 
-This is an ad hoc upload of calls generated by [SomaticWrapper v1.5](https://github.com/ding-lab/somaticwrapper) 
-and is provided for backwards compatiblity with prior SomaticWrapper calls.
-`WXS_Somatic_Variant` pipeline above (based on TinDaisy) is expected to
-ultimately replace these calls.
+Generated by [SomaticWrapper](https://github.com/ding-lab/somaticwrapper).