Opened 12 months ago
Closed 11 months ago
#1543 closed task (fixed)
Release exporter changes due to WGS data
Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
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Priority: | major | Milestone: | Reggie v4.51 |
Component: | net.sf.basedb.reggie | Keywords: | |
Cc: |
Description (last modified by )
We should include some WGS data in the next release. The starting point is existing BloodDNA
(normal) and DNA
(tumor) items that are already included in the release.
From the DNA items we go down to Library
items. Extra aliquots inbetween are skipped.
From Library
we skip the MergedSequences
and go directly to AlignedSequences
.
Then, we can add both CopyNumber
items and VariantCall
items as child items to the AlignedSequences
items.
Relevant annotations should be included in the release. From library:
- Pipeline
- ExternalOperator
From alignments:
- Pipeline
- DataFilesFolder
- ALIGNED_BASES
- ALIGNED_PAIRS
- FRACTION_DUPLICATION
- FRACTION_OPTICAL_DUPLICATION
- FragmentSizeAvg
- FragmentSizeStdev
- MEAN_COVERAGE
- SD_COVERAGE
- PF_BASES
- PF_Q30_BASES
- QC_GenoTypeHET_PCT
- AlignmentSoftware
- READS (from the parent MergedSequences)
Files that should be included from alignments items:
- alignment.bam
- alignment.bai
From ASCAT items:
- Pipeline
- DataFilesFolder
- ImbalanceTest
- Penalty
- PsiManual
- RhoManual
- TauManual
- Ploidy
- Purity
- NormalContamination
- GoodnessOfFit
- GI_Score
- LOH_fraction
- NonAberrant
Files from ASCAT items:
- ASCATprofile.png
- ASPCF.png
- germline.png
- normal_baf.txt
- normal_logr.txt
- rawprofile.png
- segments.txt
- segments_raw.txt
- stats.txt
- sunrise.png
- tumor.png
- tumor_baf.txt
- tumor_logr.txt
From VariantCall items:
- Pipeline
- DataFilesFolder
- CallableBases
- PanelOfNormals
- VariantsRaw
- VariantsPassedFilter
- Variants_FDR_Est
- Variants_Sensitivity_Est
- Variants_FP_Est
- Variants_FN_Est
- VariantsFilterThreshold
- F_SCORE_BETA
Files from VariantCall items:
- variants-somatic.vcf.gz
- variants-somatic.vcf.gz.tbi
- filtering-stats.txt
- segments.table
- SBS_96.txt
- SBS_96.pdf
Change History (19)
comment:1 by , 12 months ago
comment:6 by , 12 months ago
Description: | modified (diff) |
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comment:9 by , 12 months ago
Description: | modified (diff) |
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comment:13 by , 12 months ago
Description: | modified (diff) |
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comment:15 by , 12 months ago
Description: | modified (diff) |
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comment:18 by , 11 months ago
Description: | modified (diff) |
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comment:19 by , 11 months ago
Resolution: | → fixed |
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Status: | new → closed |
In 7454: