User: sviatoslav.kendall
sviatoslav.kendall • 510
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Posts by sviatoslav.kendall
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Comment:
C: Strelka2 and single tumour sample
... I think you could probably run Strelka2's germline workflow to at least find variants that differ from your reference genome.
https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md#germline ...
written 6 weeks ago by
sviatoslav.kendall • 510
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... I'm going to be looking at cancers that haven't been studied so thoroughly.
I've already reached out to either the authors or people involved with maintaining the software I mentioned to ask about work-arounds and planned upgrades - haven't heard back from anyone yet. I thought this issue might ha ...
written 5 months ago by
sviatoslav.kendall • 510
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... I'm interested in detecting driver genes in some cancer biopsies that have been sequenced using hg38 as the reference. I've looked at three programs so far ([MutSig2CV][1], [MuSiC][2] and [2020+][3]) and found clear indications that two of these only support hg19 and I have not found an answer in th ...
written 5 months ago by
sviatoslav.kendall • 510
• updated
4 months ago by
arvind.shankar3 • 0
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... I'm working with some exome-sequencing data that's been run through a mutation calling pipeline. My goal is determine which samples have deactivating mutations within a subset of genes. Using the [MAF][1] column "Variant_Classification", I've already decided to mutations with values like "stop_gaine ...
written 20 months ago by
sviatoslav.kendall • 510
• updated
20 months ago by
WouterDeCoster ♦ 42k
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... I've got some sequencing data (tumor/normal pairs) that has had mutations called and also been subjected to copy number analysis using [FACETS][1]; these two analyses have been merged such that each mutation has been mapped to a FACETS segment and the associated values.
I want to run an analysis t ...
written 2.6 years ago by
sviatoslav.kendall • 510
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... I have a list of mutations and want to filter out mutations that are non-diploid or have been amplified or deleted.
The data I'm working with had mutations called using [MuTect][1] and copy-number data produced using [Sequenza][2].
I do not have access to the raw sequencing data so I can't re-ru ...
written 2.6 years ago by
sviatoslav.kendall • 510
• updated
2.5 years ago by
Biostar ♦♦ 20
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... I think you should be OK doing that but pay attention to which reference genome you're using. I think the 27K probes might be based on an older build than the 450K. ...
written 2.7 years ago by
sviatoslav.kendall • 510
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... When I do survival analysis with a continuous variable as the predictor, I use the coxph() function something like this:
coxph_obj = coxph(Surv(my_Data$Survival_Time, my_Data$Survival_Event) ~ my_Data$Continous_Variable)
But here's an older post that you might find helpful: https://www.biostar ...
written 2.8 years ago by
sviatoslav.kendall • 510
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Comment:
C: Colors in IGV
... The link to IGVs default-color documentation did not work for me but it looks like it was point to [this page][1]
[1]: http://software.broadinstitute.org/software/igv/AlignmentData ...
written 3.0 years ago by
sviatoslav.kendall • 510
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... I'm writing a script that will identify loss of function mutations in a [SNPEFF][1]-annotated MAF file containing point mutations, indels or, in some cases, both.
So far, I've been doing this is by typing up a list of every [Sequence Ontology][2] value that indicates a loss of function:
stop_gaine ...
written 3.2 years ago by
sviatoslav.kendall • 510
• updated
3.1 years ago by
Biostar ♦♦ 20
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