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User: markus.riester

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Posts by markus.riester

<prev • 31 results • page 1 of 4 • next >
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Answer: A: How to use result of CNVkit to estimate purity by PureCN
... Have a look at the vignette available at https://bioconductor.org/packages/devel/bioc/vignettes/PureCN/inst/doc/Quick.pdf There is an CNVkit example at the end of the vignette. Make sure to use version 1.10.0 or current GitHub or Bioconductor devel. It currently works best with Mutect 1.1.7. It's ...
written 6 weeks ago by markus.riester • 270
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Answer: A: Calling somatic muttaions in pediatric tumor samples without matched normal samp
... Do you have a few normal samples sequenced using the same capture kit? Ideally sequenced in the same lab, but not necessarily. If yes, then our [PureCN][1] tool might be worth a look. There is a downstream script (Dx.R) that calculates TMB and somatic signatures for tumor-only samples. But not sure ...
written 4 months ago by markus.riester • 270
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Comment: C: Mutect2 filtering log-odds (LOD) threshold
... You usually want to have a fixed assay-specific error rate. They just used this example to put the number in context. But sure, if you can tolerate more false positives when you are working in CRC, nothing prevents you from setting cutoffs accordingly. ...
written 6 months ago by markus.riester • 270
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Comment: C: TMB Tumor Mutation Burden
... Instead of using 30 as denominator, I would use tools like GATK CallableLoci to get the exact number of bases. ...
written 8 months ago by markus.riester • 270
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Comment: C: Infer somatic mutations without normal control
... Apologies for the late response, just saw this. 4) I'm just saying that this filter will under some circumstances remove somatic variants. But yes, in most cases, especially low purity samples, you will be fine. But for the proper way, see 7 (see [here][1] for another recent paper). Cross-sample c ...
written 8 months ago by markus.riester • 270
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Answer: A: Infer somatic mutations without normal control
... 1. I assume you are talking about high coverage data? Then yes, ad hoc, but pretty standard. Ideally one examines the coverage of the assay over many samples and understands why some regions have low coverage. Then understand how this impacts your variant calling. 2. Should be fine. 3. Depends w ...
written 9 months ago by markus.riester • 270
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Answer: A: WES chromosome Y off-target reads coverage compare to autosome
... Should be much lower because of the very low mappability of chrY. If you have WES, then why using off-target reads? For most kits, you will have plenty of perfectly mapping exons that will show 0 reads in females (or very few in case of minor cross-sample contamination). ...
written 9 months ago by markus.riester • 270
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Answer: A: Suggestions regarding bioinformatics journal
... If the critique of reviewer 3 has absolutely no merit, I would consider an appeal. It was probably a very tough decision for the editor as well, so he might be willing to hear your case again. Be nice, admit the flaws in presentation etc. 8 months until rejection is a worst case scenario, but stil ...
written 10 months ago by markus.riester • 270
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Answer: A: ABSOLUTE R package - CreateReviewObject Error, Error in seq_len(M) : argument mu
... I cannot comment on the crash, but I recommend reading the [ABSOLUTE][1], [ASCAT][2] and more recent papers like [Sequenza][3]. Running ABSOLUTE with only segmented data is pretty much futile. You need germline allelic fractions to determine the number of maternal and paternal copy numbers, which ar ...
written 12 months ago by markus.riester • 270
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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 13 months ago by markus.riester • 270

Latest awards to markus.riester

Scholar 13 months ago, created an answer that has been accepted. For A: Somatic variant caller
Good Answer 15 months 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 15 months ago, created an answer that has been accepted. For A: Somatic variant caller
Appreciated 15 months ago, created a post with more than 5 votes. For A: WES or WGS analysis of cancer samples with no matched germline
Scholar 15 months ago, created an answer that has been accepted. For A: Somatic variant caller
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Somatic variant caller
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Somatic variant caller
Scholar 19 months ago, created an answer that has been accepted. For A: Somatic variant caller
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