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DCC Analysis Summary files

Files here provide a unified summary of all Year 2 and later CPTAC3 genomic analysis results and their location on CPTAC-DCC.

Format

DCC Analysis Summary files have the following initial columns:

 1. case
 2. disease
 3. pipeline_name
 4. pipeline_version
 5. timestamp
 6. C3Y 
 7. DCC_path
 8. filesize
 9. file_format
10. md5sum

NEW: Column C3Y indicates "CPTAC3 Year" and takes values Y1, Y2, etc. It is used for administrative purposes.

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.

Pipeline AML CCRCC CM GBM HNSCC LSCC LUAD PDA SAR UCEC Total
Methylation Array 43 222 8 116 111 113 229 164 19 246 1271
miRNA-Seq 42 222 8 114 111 113 229 164 19 247 1269
miRNA-Seq QC 11 28 5 52 17 27 10 77 19 39 285
RNA-Seq Expression 11 221 8 114 111 113 164 164 19 181 1106
RNA-Seq Fusion 11 112 8 119 111 113 164 83 19 77 817
RNA-Seq Transcript + Splicing 1 112 3 119 111 113 53 83 0 77 672
RNA-Seq QC 11 112 8 119 111 113 53 83 19 77 706
WGS SV 0 0 0 59 109 * 113 111 77 0 39 508
WGS CNV Somatic 0 117 0 59 21 113 121 77 0 39 547
WGS QC 0 0 0 60 21 113 0 77 0 39 310
WXS MSI 0 105 0 118 111 113 111 0 0 143 701
WXS Normal Adjacent 0 80 0 0 5 22 101 0 0 21 229
WXS QC 5 87 4 118 111 113 101 44 9 51 643
WXS Somatic 0 0 0 0 0 113 0 0 0 0 113
WXS Somatic SW 0 0 0 0 0 113 109 0 0 0 222

Last update: 2/19/20

  • HNSCC WGS SV analysis is ad hoc analysis of data aligned by UMich to custom reference.

Year 1

Processing performed during CPTAC3 Year 1 consisted analyses for CCRCC, LUAD, and UCEC discovery cohort, and a visual summary of processing per batch can be found in this processing update description. A subset of Year 1 calls is included in the DCC analysis summaries here, mainly those calls whose pipeline versions are consistent with those in Year 2. Year 1 analyses can be identified by "Y1" in C3Y column, and do not have details about input data.

Pipeline details

Details and notes about pipelines and processing status below. More complete 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 Methylation_Array.DCC_analysis_summary.dat

CPTAC3 Methylation pipeline details

miRNA-Seq

miRNA-Seq analysis

Analysis details miRNA-Seq.DCC_analysis_summary.dat Note that each sample has results for mature miRNA, precursor miRNA, and total miRNA.

miRNA-Seq pipeline documentation and processing description.

miRNA-Seq QC

Analysis details miRNA-Seq_QC.DCC_analysis_summary.dat

QC pipeline documentation

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

CPTAC3 RNA-Seq Expression pipeline

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, and pipeline documentation on GitHub

RNA-Seq Transcript + Splicing

Analysis details RNA-Seq_Transcript.DCC_analysis_summary.dat

Pipeline documentation on GitHub

RNA-Seq QC

Analysis details RNA-Seq_QC.DCC_analysis_summary.dat

QC pipeline documentation

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

CPTAC3 SomaticSV pipeline on GitHub

WGS CNV Somatic

Analysis details WGS_CNV_Somatic.DCC_analysis_summary.dat

WGS CNV pipeline

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

CPTAC3 QC pipeline

WXS

WXS MSI

Analysis details WXS_MSI.DCC_analysis_summary.dat

WXS MSI pipeline on GitHub

WXS Normal Adjacent

Analysis details WXS_Normal_Adjacent.DCC_analysis_summary.dat

WXS Normal Adjacent analysis generated using TinDaisy pipeline

WXS QC

Analysis details WXS_QC.DCC_analysis_summary.dat

CPTAC3 QC pipeline

WXS Somatic

WXS Somatic analysis is new for CPTAC3 Year 3. So far only 113 LSCC cases have been analyzed using TinDaisy variant caller v2.1

Analysis details WXS_Somatic.DCC_analysis_summary.dat

WXS Somatic SW

113 LSCC and 109 LUAD cases in WXS_Somatic_Variant_SW.DCC_analysis_summary.dat.

This is an ad hoc upload of calls generated by SomaticWrapper v1.5 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.