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User: markus.riester

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Posts by markus.riester

<prev • 16 results • page 1 of 2 • next >
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Comment: C: WES or WGS analysis of cancer samples with no matched germline
... Just run in without the normal BAM. The GATK3 version of MuTect2 doesn't officially support tumor-only analyses, but will do it. For GATK4beta, it's described in the documentation. ...
written 10 days ago by markus.riester • 180
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Answer: A: WES or WGS analysis of cancer samples with no matched germline
... MuTect and FreeBayes for SNVs are probably the most used tools for tumor-only analyses. Copy number, if you have some normals, you can try CNVkit, cn.mops (I think) and GATK4beta. If you need purity/ploidy and want to classify variants as germline vs somatic, there isn't much out yet, so we wrote ou ...
written 11 days ago by markus.riester • 180
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Answer: A: Tumor Mutation Burden calculation: all_mut vs non_synonym
... Correlation is a rather poor evaluation metric this case, since it can be driven by hyper-mutated outliers that are easy to get right with small panels, i.e. the correlation depends on both the mutation rate and the panel size. Including silent mutations will give you a more accurate total somatic ...
written 12 days ago by markus.riester • 180
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Comment: C: Detecting CNV can't cover aneuploidy situation
... Maybe important to add that in whole-exome data, because you only sequence 1-2% of the genome, you don't see most of the breakpoints directly. So you are pretty much left with read-pileups. Then there is unfortuantely a huge variance in quality of whole-exome data. Great sequencing centers get cov ...
written 12 days ago by markus.riester • 180
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Comment: C: "Shifted" copy number ratios coming from cnvkit?
... Yeah, it's not 100% clear from the plots, because it looks like the log ratios are not weighted by segment size. But the first peak is always higher than the third+ (assuming the second corresponds to normal 2). That's all. ...
written 6 weeks ago by markus.riester • 180
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Answer: A: "Shifted" copy number ratios coming from cnvkit?
... When copy number ratios are calculated, you need to normalize tumor and normal for sequencing coverage differences. The problem is, however, that tumor cells can have more or less DNA than normal. Since you don't know the ploidy (average tumor copy number) when you calculate the log-ratios, you cann ...
written 6 weeks ago by markus.riester • 180
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Comment: C: Is there a consensus that Matlab is the wrong language for open-access bioinform
... A reviewer who rejects your paper because of the choice of the programming language does not understand the role of peer review. Having said that, there is a lot of benefit for both you and your users in providing your code in a public repository with automated builds and unit tests. Make it as ea ...
written 4 months ago by markus.riester • 180
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Answer: A: Comparison of exome variant allele frequencies
... It is an oversimplification. Allelic fractions are a function of tumor purity, allele-specific copy number, cellular fractions (percentage of tumor cells with mutation), and mapping biases. You are probably interested in a differences of cellular fraction, so you need to adjust for any differences i ...
written 4 months ago by markus.riester • 180
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Answer: A: Copy Number Variation Tools
... There are a couple of good reviews with links to all important tools, for example a fairly recent one is https://doi.org/10.1093/bib/bbv055. There is no gold standard and different tools were optimized for very different scenarios. Some tools require matched normals. Some use pool of normals for b ...
written 4 months ago by markus.riester • 180
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Answer: A: Somatic variant caller
... The variant caller assumes sequencing errors are Poisson distributed. Looks like you get a call when the alt allele has a less than 1% chance of being a sequencing error given the number of supporting reads and the predefined error rate. ...
written 4 months ago by markus.riester • 180

Latest awards to markus.riester

Good Answer 10 days ago, created an answer that was upvoted at least 5 times. For A: WES or WGS analysis of cancer samples with no matched germline
Scholar 10 days ago, created an answer that has been accepted. For A: Somatic variant caller
Appreciated 11 days ago, created a post with more than 5 votes. For A: WES or WGS analysis of cancer samples with no matched germline
Scholar 11 days ago, created an answer that has been accepted. For A: Somatic variant caller
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: Somatic variant caller
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Somatic variant caller
Scholar 4 months ago, created an answer that has been accepted. For A: Somatic variant caller
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