User: markus.riester

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Posts by markus.riester

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Answer: A: Something wrong with my Bioconductor installation? ggtree cannot read any tree
... See the documentation of ?system.file. nwk <- "/home/ubuntuser/Desktop/Geospiza.nex" ...
written 19 minutes ago by markus.riester60
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Comment: C: Understanding PureCN and its germline SNPs
... It is currently only supporting either tumor-only or tumor/normal VCFs. Feel free to add a feature request on GitHub. PureCN is currently not supporting multiple time points (or regions) per sample, so a multi-sample VCF doesn't provide anything that would be used. But this might change in the futur ...
written 11 days ago by markus.riester60
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Answer: A: Understanding PureCN and its germline SNPs
... Somatic copy number events most often result in an unbalanced number of maternal and paternal chromosomes. That in turn results in allelic imbalance of germline SNPs we can easily detect in tumor. SNPs thus help us to get the ploidy right. PureCN was mainly written for tumor-only VCFs that include ...
written 14 days ago by markus.riester60
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Answer: A: PureCN support for indels
... You'll need the developer version for experimental indel support (https://github.com/lima1/PureCN). Give it a try and let me know if you run into problems. ...
written 14 days ago by markus.riester60
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Answer: A: Standardizing gene symbols
... For human symbols, HGNChelper might work for you:     checkGeneSymbols(c("TAU", "MTBT1","MAPTL"))       x Approved Suggested.Symbol 1   TAU    FALSE             MAPT 2 MTBT1    FALSE             MAPT 3 MAPTL    FALSE             MAPT Warning message: In checkGeneSymbols(c("TAU", "MTBT1", "MAP ...
written 4 months ago by markus.riester60 • updated 4 months ago by Gordon Smyth33k
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Comment: C: errors in version 1.7.53
... Sorry to hear that. Negative counts shouldn't happen, it could be an integer overflow. We can debug offline via email (markus.riester at novartis com). If you can send me an example coverage file (loess normalized) plus the gc.gene.file, that would be great. If this is from a custom panel you don't ...
written 6 months ago by markus.riester60
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Comment: C: errors in version 1.7.53
... Hi, I didn't increase in the version number because 1.7.55 wasn't build yet in Bioconductor 3.6.  ...
written 6 months ago by markus.riester60
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Comment: C: errors in version 1.7.53
... I hope this fixed now. The Mutect2 detection should be more robust and is not attempted at all if you provide the Mutect1 stats file. Can you re-try after biocLite("lima1/PureCN")? ...
written 6 months ago by markus.riester60
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Comment: C: errors in version 1.7.53
... Okay, never seen this before, but yes, looks like a bug. I'll try to reproduce. If you can share an example VCF (even if it only contains a single variant) that would be helpful. Thanks for the report. ...
written 6 months ago by markus.riester60
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Answer: A: errors in version 1.7.53
... If your VCF is generated by Mutect2, then this might be related to a bug in filterVcfMuTect2 that I just fixed yesterday in GitHub. This function is new and is supposed to filter variants by various Mutect2 flags, but wrongly removed all variants when unfiltered VCF was provided. Please note that on ...
written 6 months ago by markus.riester60

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