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Similar to pathology, are there example disease groups for Cytogenetics? Like how pathology has 'brain' and 'head_neck'.
On inspecting `process.py` there is a comment saying "disease specific cytog…
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Here is one such file: https://dcc.icgc.org/repositories/files/FI743257. It is originated from EGA, we transferred to Collaboratory, but the file page only shows this file exist in Collab but not in E…
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I am looking to run Hotspot to discover transcriptional modules in a dataset containing integrated data from over 20 samples. All of the Hotspot vignettes I see online only analyze data from a single …
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How would someone extract the schema specific data needed in order to populate lists of all of the possible values for the pathological, and clinical values for the T, N, M, and Stage Group fields? S…
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## Feature request
### Tool(s) or class(es) involved
mutect2.wdl and related scripts
### Description
It would be useful to have multi-sample calling support (#5560) in M2 WDL.
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## Bug Report
### Affected tool(s) or class(es)
_Mutect2_
### Affected version(s)
- [x] version 4.1.5.0~4.1.8.1
### Description
`RNA-Seq data` → `STAR alignment` → `MarkDuplicates` → `S…
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Hi,
I saw Ploidetect requires the definition of snp array. Is that used for allele-specific CNV calling?
If that is, can I replace the array by germline SNV sites or some common snp from dbSNP?
…
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In the last revision (and perhaps some earlier ones) the option -M in var2vcf_paired.pl doesn't seem to have any effect on the output. I cross-tested the outputs from the new previous tool with an old…
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Hello,
I wanted to download Splice Junction files for the Primary Tumors of the TCGA-GBM project. I am runnin g R 4.0.0.
I used the command
`query The columns of the SJ.out.tab file have the follo…