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User: markus.riester

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Posts by markus.riester

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Tumor purity estimation by allele frequency of COSMIC identified somatic mutatio
... Partly because they don't adjust for purity and copy number, as they state in the Discussion. With normal contamination, there are ways to discriminate somatic from germline. At least there are ways to calculate those probabilities accurately. ...
written 15 days ago by markus.riester • 210
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Answer: A: CNV calls in VCF format, conversion to PCAWG-11 Calibration
... - Yes, "pos" should be start. - "major_cn" is total copy number - minor_cn (major+minor=total, minor <= major) - cellular_prevelance is the fraction of tumor cells with this alteration. Looks like your tool does not report this value. You can set to 1. There are a gazillion VCF parsers and li ...
written 18 days ago by markus.riester • 210
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Comment: C: tumor only variant calling tools
... That is exactly implemented in https://doi.org/10.1186/s13029-016-0060-z (https://bioconductor.org/packages/devel/bioc/html/PureCN.html). For targeted panels, this will only work if you have sufficiently large pool of normals, even coverage and either hybrid capture data (gives you off-target read ...
written 22 days ago by markus.riester • 210
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Comment: C: tumor only variant calling tools
... Depends. Most clinical FFPE samples have low purity (typically well <75%) and high coverage. Their SGZ algorithm (cited in https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-017-0424-2) then adjusts allelic fractions for purity, ploidy and local copy number. Our PureCN is fairly s ...
written 22 days ago by markus.riester • 210
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Answer: A: WES samples failing ABSOLUTE
... Looks like the copy number ratios are not in the expected format and range. Check that ABSOLUTE knows that you are providing total copy number ratios and not allele-specific (HAPSEG) ones, i.e. set copy_num_type argument to "total". Make sure that they are correctly log-transformed. As a general re ...
written 4 weeks ago by markus.riester • 210
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Answer: A: Merging CNVs from multiple tumor samples from the same patient
... I think superFreq (https://github.com/ChristofferFlensburg/superFreq) is pretty much the only allele-specific caller designed for multiple samples. In case your data is from whole-genomes, there might be others. The benefit of supporting multiple samples is mostly in tracking cellular fractions of ...
written 4 weeks ago by markus.riester • 210
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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 9 weeks ago by markus.riester • 210
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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 9 weeks ago by markus.riester • 210
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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 10 weeks ago by markus.riester • 210
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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 10 weeks ago by markus.riester • 210

Latest awards to markus.riester

Scholar 18 days ago, created an answer that has been accepted. For A: Somatic variant caller
Good Answer 9 weeks 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 9 weeks ago, created an answer that has been accepted. For A: Somatic variant caller
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: WES or WGS analysis of cancer samples with no matched germline
Scholar 9 weeks ago, created an answer that has been accepted. For A: Somatic variant caller
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Somatic variant caller
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Somatic variant caller
Scholar 6 months ago, created an answer that has been accepted. For A: Somatic variant caller
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