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Tasks needed prior to CCS handoff
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_Tasks needed to complete before Manhattan pipeline gets handed off for testing and CCS runs_
#268 Implementing GetBaseCountsMultipSample
#138/#215 LOHHLA …
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GIven the interest in studies that involve tumor heterogeneity / subclonality, currently bcbio offers "out of the box" support for both somatic variants and CNVs. A useful metric that can be combined …
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Here is partial output of a cell from `filtered_BCR_seqs/fitlered_BCRs.txt`:
```
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test
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BCR_H recombinants: 0/1
BCR_K recombinants: 0/2
BCR_L recombinants: 0…
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I've been running some vignette code (specifically this code https://github.com/caravagn/revolver.misc/blob/master/vignette_plotting_functions/vignette_plotting_functions.md) . During the issue of a…
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@marcjwilliams1 First off, thanks for making this resource available as a companion to your paper, very helpful. The suggested neutralitytestr approach seems to be including read-depth, cellularity, …
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Hi BraCeR team,
Thank you for the previous solutions which are work!
I use FASTQ file containing #1 and #2 mates from paired-end sequencing generated from 10x genomic system. This sample suppos…
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(`collapseMatrix` is scheduled to be moved from Rcompadre to Rage, as per jonesor/Rcompadre#28)
The documentation for `collapseMatrix` contains the note:
> Note: this function is only valid for …
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hi, chris.
Now, I have converted some CNV to pseudo-VAF. And I combined the SSM with pseudo-VAF for clonal analysis by Sciclone. I always get 3 clones by different maxmumClusters (see fig as below).…
moshl updated
6 years ago
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Hello,
The input vcf for PureCN should contain both germline and somatic variants. Does this mean both the germline and somatic vcf from variant caller should be combined together into a single one…
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I have followed the "getting started" instructions in the [vignette](https://jdblischak.github.io/workflowr/articles/wflow-01-getting-started.html) precisely, using `workflowr` 1.1.1 and R 3.5.1.
E…