DCC_Analysis_Summary

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

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. 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 unique cases processed per disease and pipeline. Last updated 9/21/22.

Pipeline	AML	CCRCC	CM	GBM	HNSCC	LSCC	LUAD	PDA	SAR	UCEC	Total
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

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

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.

RNA-Seq

RNA-Seq Expression

Analysis details RNA-Seq_Expression.DCC_analysis_summary.dat

CPTAC3 RNA-Seq Expression pipeline

RNA-Seq Fusion

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

WGS

WGS SV

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

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 Somatic TD

WXS Somatic analysis TinDaisy variant caller v2.1

Analysis details [WXS_Somatic_Variant_TD.DCC_analysis_summary.dat](WXS_Somatic_Variant_TD.DCC_analysis_summary.dat"

WXS Somatic SW

WXS_Somatic_Variant_SW.DCC_analysis_summary.dat.

Generated by SomaticWrapper.