User: markus.riester
markus.riester • 470
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Posts by markus.riester
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... 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 weeks ago by
markus.riester • 470
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... It currently does not take all GATK4 output files out-of-the-box, but you can provide the segmentation and copy number log-ratios (see Section 10.1). PureCN can read GATK4 coverage files (in hdf5 format). Simply provide the tumor coverage and PureCN will be able to map provided log-ratios to the gen ...
written 5 weeks ago by
markus.riester • 470
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... You mead adjusting the measured log2-ratio for purity and ploidy? ABSOLUTE and similar algorithms calculate integer copy numbers for all segments. If you need adjusted log-ratios, you can do some simple algebra (see [Zack et al.][1]). End result is that diploid regions are 0 centered (because log2(2 ...
written 5 weeks ago by
markus.riester • 470
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... In a regression, I would probably just use a gene-level log-ratio, ideally purity and ploidy adjusted, see for example [Zack et al.][1]. CCFs of CNAs are tricky, except maybe for single deletions and gains, so be careful here, GIGO. If ploidy adjustment has a big impact, then maybe what you are seei ...
written 5 weeks ago by
markus.riester • 470
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... Yes, this FACETS heuristic to find the diploid state works very well in the majority of cases, but indeed fails in cases without clear diploid state (it warns you though). The alternative is trying all reasonable purity and ploidy cases (e.g. what Sequenza and many others do), at the cost of larger ...
written 5 weeks ago by
markus.riester • 470
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... Since you link an old response of mine:
1). When you say you have CNV calls, I assume segmented log2 tumor/normal coverage ratios, obtained by tools like CNVkit, Control-Freec, GATK etc.. The measured log2-ratios are a function of copy number, purity and ploidy; copy number obviously increases cov ...
written 5 weeks ago by
markus.riester • 470
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... The normalization algorithms assume that test and control cells contain the same amount of DNA. In your case, the test ploidy is significantly below 2, thus you get a right shift in log2-ratios. Have a look at tools like [ABSOLUTE][1] or [ASCAT][2] that assign integer copy numbers to these peaks by ...
written 7 weeks ago by
markus.riester • 470
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... 1) The .cnr files
2) You run Mutect as you normally would, i.e. provide the normal BAM file and you can also provide --normal_panel for artifact flagging. --statfile is optional, but since Mutect automatically generates it it's easy to add. When provided, PureCN can remove artifacts based on the fl ...
written 9 weeks ago by
markus.riester • 470
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... Exactly. The PoN should normalize the coverage well. You might see a higher average coverage variance in the backbone due to the lower coverage (resulting in higher log-ratio noise), but with >100X this should be minor and most recent tools including CNVkit can incorporate this in the segmentatio ...
written 9 weeks ago by
markus.riester • 470
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... No experience with the IDT backbone, but yes, it makes sense to spike in the backbone lower. Usually you add single baits for the SNPs and multiple baits for each target in your 31 genes.
You want the backbone targets included since those are enriched in heterozygous SNPs and will thus help with L ...
written 10 weeks ago by
markus.riester • 470
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