User: markus.riester
markus.riester • 320
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Posts by markus.riester
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... No idea, I would ask their support. ...
written 7 days ago by
markus.riester • 320
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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.riester • 320
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... Are the BAM files aligned to the same FASTA file that was used to generate the interval file? ...
written 14 days ago by
markus.riester • 320
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... 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.riester • 320
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... 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.riester • 320
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... 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.riester • 320
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... 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.riester • 320
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... 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.riester • 320
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... 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.riester • 320
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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.riester • 320
Latest awards to markus.riester
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created an answer that was upvoted at least 5 times.
For A: WES or WGS analysis of cancer samples with no matched germline
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20 months ago,
created a post with more than 5 votes.
For A: WES or WGS analysis of cancer samples with no matched germline
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