User: markus.riester

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Posts by markus.riester

<prev • 58 results • page 1 of 6 • next >
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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 22 days ago by markus.riester480
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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 23 days ago by markus.riester480
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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 24 days ago by markus.riester480
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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 3 months ago by markus.riester480
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Comment: C: Library size normalization during CNV calling from genomically doubled tumor tis
... A perfectly doubled genome couldn't be distinguished from normal, but chromosomal instability by definition results in many gains and losses. In simple terms, algorithms designed for this problem see that it cannot be a copy number of 2 when there are extensive losses that would correspond to copy n ...
written 3 months ago by markus.riester480
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Comment: C: Library size normalization during CNV calling from genomically doubled tumor tis
... ? Allele frequencies are used in these algorithms to eliminate wrong purity and ploidy combinations. ...
written 3 months ago by markus.riester480
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Answer: A: Library size normalization during CNV calling from genomically doubled tumor tis
... Every purity and ploidy aware copy number caller takes this into account. Have a look at the ASCAT or ABSOLUTE paper. ...
written 3 months ago by markus.riester480
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Comment: C: How to use result of CNVkit to estimate purity by PureCN
... PureCN version 1.15.4 now added support for the GATK4 copy number workflow. ...
written 3 months ago by markus.riester480
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Answer: A: Effect size in power analysis when dealing with Poisson based variant caller
... Such a power calculation is described in [Carter el al][1]. You can find a well documented implementation in our [PureCN][2] R package. Essentially this calculates the probability of sampling sufficient supporting reads so that you can rule out a sequencing error. [1]: https://www.nature.com/ar ...
written 4 months ago by markus.riester480
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Comment: C: How to use result of CNVkit to estimate purity by PureCN
... When you calculate the log-ratio like that, you are not using GATK4's denoising steps. GATK4 should generate a file with log2-ratio, you want to parse that file and provide the corresponding log2-ratio like you did. The issue is likely the wrong format of the interval file. Just run it with: r ...
written 5 months ago by markus.riester480

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