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That is, multiple samples of the same tumor in space or time, a tumor and a metastasis, a tumor and its cfDNA etc.
First we have to ask collaborators and the community what features they would like…
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Hi Dinh,
I would like to ask you a question.I have bisulfite sequencing data from cfDNA captrued with target probe.Therefore,for a specific region,the haplotypes may have different start and end as…
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Hi,
I have been trying to call variants on liquid biopsy samples using the variantCaller (TVC) 5.10.0.18 -and then with 5.10.0.20 from within Ion Torrent Suite (ITS) server web interface applicatio…
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I'm seeing error messages relating to certain reads that seem unremarkable except that they contain N's. Like this:
```
Z/r/job6pcRlf [2017-07-05T15:44:45.538328] [blade15-1-16.gsc.wustl.edu] …
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I've some maternal blood cfDNA (containing both maternal and fetal DNAs) sequenced bam files. Whether this method can be used for predicting fetal sex?
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This is most probably an issue upstream with the data submission.
Example:
https://www.targetvalidation.org/evidence/ENSG00000133703/EFO_0000096
Title of the abstract: Circulating tumour DNA seque…
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My samples have rather low purity, because these are gastric cancer tumors and it is typical for the tumor to be diffuse. Consequently, PureCN makes a lot of calls of purity = 0.15, and many of my sa…
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Hi Felix,
Another question for you -- I'm looking at M-bias for my samples (8-10x WGBS) and I'm noticing that there is definitely a dropoff of methylation at the start of the read, but it goes back…
caalo updated
6 years ago
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Currently bcbio installs 4.0.3.0, but the latest changes in 4.0.5.2 and before (https://github.com/broadinstitute/gatk//releases) offer quite a number of improvements in particular with MuTect2 specif…
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@davidbenjamin commented on [Wed Feb 15 2017](https://github.com/broadinstitute/gatk-protected/issues/903)
Since most of the work is in setting up the necessary tools and pipelines to evaluate, I wil…