User: markus.riester

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Posts by markus.riester

<prev • 37 results • page 1 of 4 • next >
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Comment: C: PureCN: Estimating tumor purity and ploidy
... No idea, I would ask their support. ...
written 7 days ago by markus.riester320
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Answer: A: Pool of Normals- PureCN
... Have a look at the FAQ section in the vignette. There is a section about pool of normals. For coverage normalization, no, you cannot mix different capture kits. Use as many normals as you have. You can use technical replicates for coverage normalization, i.e. they do not need to be from different ...
written 7 days ago by markus.riester320
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Comment: C: PureCN: Estimating tumor purity and ploidy
... Are the BAM files aligned to the same FASTA file that was used to generate the interval file? ...
written 14 days ago by markus.riester320
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Comment: C: PureCN: Tool for estimation of tumor purity and ploidy
... Both builds are supported. Please try to create a reproducible example, like a minimal BED file and open an GitHub issue. Thank you. ...
written 14 days ago by markus.riester320
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Answer: A: PureCN: Tool for estimation of tumor purity and ploidy
... Hi, the infile needs to be a BED file with the capture baits. This file should only contain regular chromosomes. If it does, please open a GitHub issue at https://github.com/lima1/PureCN/issues, ideally including a minimal BED file to reproduce the issue. Thanks a lot, Markus ...
written 16 days ago by markus.riester320
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Answer: A: Are the somatic mutations in TCGA filtered for germline mutations?
... They sequenced matched normals, so yes, it is the case. Have a look at the detailed papers associated with each TCGA dataset. ...
written 5 weeks ago by markus.riester320
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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 months ago by markus.riester320
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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 9 months ago by markus.riester320
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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 12 months ago by markus.riester320
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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 13 months ago by markus.riester320

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