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User: markus.riester

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Posts by markus.riester

<prev • 29 results • page 1 of 3 • next >
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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 4 weeks ago by markus.riester • 240
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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 9 weeks ago by markus.riester • 240
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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 9 weeks ago by markus.riester • 240
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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 3 months ago by markus.riester • 240
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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 3 months ago by markus.riester • 240
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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 4 months ago by markus.riester • 240
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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 6 months ago by markus.riester • 240
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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 7 months ago by markus.riester • 240
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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 7 months ago by markus.riester • 240
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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 7 months ago by markus.riester • 240

Latest awards to markus.riester

Scholar 7 months ago, created an answer that has been accepted. For A: Somatic variant caller
Good Answer 9 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 9 months ago, created an answer that has been accepted. For A: Somatic variant caller
Appreciated 9 months ago, created a post with more than 5 votes. For A: WES or WGS analysis of cancer samples with no matched germline
Scholar 9 months ago, created an answer that has been accepted. For A: Somatic variant caller
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Somatic variant caller
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Somatic variant caller
Scholar 13 months ago, created an answer that has been accepted. For A: Somatic variant caller
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