User: markus.riester

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Posts by markus.riester

<prev • 64 results • page 1 of 7 • next >
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Comment: C: PureCN prepare environment error
... Hm, this shouldn't be that difficult. Did you run samtools faidx GRCh38.d1.vd1.fa? This should probably warn you when something is wrong with the Fasta. ...
written 1 day ago by markus.riester490
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Comment: C: PureCN prepare environment error
... Glad you figured it out. Bioconductor should be able to work with uncompressed Fasta files if they are sorted (the official genome build Fasta files are). See the underlying ?scanFa function. ...
written 4 days ago by markus.riester490
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Answer: A: PureCN prepare environment error
... Hi, you sure hg38.fa is the correct path to the FASTA file? > path[1]="hg38.fa": The system cannot find the file specified ...
written 6 days ago by markus.riester490
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Answer: A: How to classify samples into high and low Tumor mutational burden?
... There is no consensus regarding cutoffs and it's probably best to use as continuous covariate when possible. https://www.ncbi.nlm.nih.gov/pubmed/30643254 ...
written 3 months ago by markus.riester490
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Answer: A: Somatic variant calling with/without matched normal sample (Mutect2)
... 4300 somatic calls would be a lot even for WES. Is it possible there is a tumor/normal misalignment? Otherwise, running it quickly with Mutect 1 would be an easy way to debug. Mutect 1 reports all variants, even if found in PoN or matched normal, so it's easier to figure out the impact of those. ...
written 4 months ago by markus.riester490
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Answer: A: estimate tumor purity from capture panel data using tumor-only mode
... If you have at least a few processed-matched normals, you can try https://github.com/lima1/PureCN (disclaimer: our tool). ...
written 7 months ago by markus.riester490
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Comment: C: Filtering for individual allelic balance in multisample vcf using GATK4
... Others are way more qualified to answer here since I'm not a germline person, but with average 10X, you have to accept that you don't have the power to detect heterozygosity for all sites. So you have to find a way to deal with the uncertainty. I'm sure there are standard ways of doing that for your ...
written 8 months ago by markus.riester490
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Comment: C: Filtering for individual allelic balance in multisample vcf using GATK4
... It probably depends for what you need allelic imbalance and how sensitive your detection of allelic imbalance needs to be. Is this RNA or DNA-seq? If the latter, what's the coverage? ...
written 8 months ago by markus.riester490
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Comment: C: Filtering for individual allelic balance in multisample vcf using GATK4
... Are you sure that's not a [XY Problem][1]? [1]: https://en.wikipedia.org/wiki/XY_problem ...
written 8 months ago by markus.riester490
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Comment: A: Library size normalization during CNV calling from genomically doubled tumor tis
... See what you mean, but I think what CY means with library size is simply total sequencing read coverage. But maybe I was interpolating too aggressively. ...
written 11 months ago by markus.riester490

Latest awards to markus.riester

Scholar 13 months ago, created an answer that has been accepted. For A: Somatic variant caller
Teacher 13 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
Scholar 14 months ago, created an answer that has been accepted. For A: Somatic variant caller
Scholar 14 months ago, created an answer that has been accepted. For A: Somatic variant caller
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Somatic variant caller
Scholar 17 months ago, created an answer that has been accepted. For A: Somatic variant caller
Scholar 2.8 years ago, created an answer that has been accepted. For A: Somatic variant caller
Good Answer 3.0 years 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 3.0 years ago, created an answer that has been accepted. For A: Somatic variant caller
Appreciated 3.0 years ago, created a post with more than 5 votes. For A: WES or WGS analysis of cancer samples with no matched germline
Scholar 3.0 years ago, created an answer that has been accepted. For A: Somatic variant caller
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Somatic variant caller
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Somatic variant caller
Scholar 3.3 years ago, created an answer that has been accepted. For A: Somatic variant caller

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