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Hi Christoffer,
1) I want to start the superFreq pipeline from variant calling that I performed using Mutect2 (we find that it identified indels pretty well) that was run on tumor-normal pairs as w…
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VRanges can manage all the information on samples and calls, but the
current function just acquires one record per variant. Is this function/package
still in development?
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Hi etal,
Thank you for this awesome algorithm, it worked well with our exome-seq data, really comparable to our aCGH data of the same sample!!
I was trying to check clonality of the sample, input as…
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Hi, I'm curious if your suggested strategy for incorporating CNA variants into a clonality analysis has changed since the the Sciclone paper in 2014. I'm looking to assign clone numbers to mutations …
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Trying to run cloneHD using my files generated from filterHD step. Running into a error without much explanation:
./build/cloneHD --cna tumor.exome.cloneHD.noY --chr normal.exome.cloneHD.noY --baf tu…
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There is something wrong with the default Illumina template files (genomics_short_reads.txt, genomics_short_reads_2.txt, transcriptomics_short_reads.txt). Using them throw the following error:
> I,…
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Hi!
I'm trying to compare different tools/methods to estimate clonality in tumors with TCGA data in order to see which samples have a clustering consensus between PyClone, Sciclone and probably Expand…
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Hi,
I have been testing SciClone as a solution to make clonality predictions for one of the datasets I am working with.
I noticed that if I run SciClone multiple times on the same sample data I get a…
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The current way PhyloWGS is distributed, it is a few C++/Pyhton/HTML utilities bind together (which is completely fine), but the current structure makes strong assumptions about the environment the to…