User: Manuel Landesfeind
Manuel Landesfeind • 1.1k
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- Göttingen, Germany
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- 10 hours ago
- Joined:
- 3 years ago
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Posts by Manuel Landesfeind
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2
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... If you have already an R package for the analysis task available and you just want to have some web-interface to make it accessible, a quick alternative might be the development of a [Shiny app][1].
Anyway, for larger and more complex projects, I recommend liux.bio's answer
[1]: https://shiny.r ...
written 20 days ago by
Manuel Landesfeind • 1.1k
1
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1
answer
145
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1
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... Some time ago I have done a comparison of WES and RNA-Seq variant calling in a setting with more samples (92) but different software (GATK vs. Samtools) for the calling (which might introduce additional bias), but I confirm that the overlap between both methods is rather low. You may want to have a ...
written 24 days ago by
Manuel Landesfeind • 1.1k
0
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0
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155
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0
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... I agree, in that case you should not use tumor as normal. But than I would still go forward with calling mutations on all samples and removing everything found in population databases with decent frequency. ...
written 3 months ago by
Manuel Landesfeind • 1.1k
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155
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... About the somatic variants: you can annotate with ExAC (or other population databases) to remove "putative germline" from your analysis. There are plenty of suggestions on Biostars already.
Second, depending on your scientific question, it might be sufficient to use the "tumor" as "normal" because y ...
written 3 months ago by
Manuel Landesfeind • 1.1k
0
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1
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14k
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1
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... The term "GRCh38" refers to the genomic assembly. The ".78" and ".91" refer to the version of gene annotation provided by Ensembl, i.e. where do introns/exons/etc start and end. To my knowledge, the genomic sequence for "GRCh38.78" and "GRCh38.91" should be identical and only the gene annotation sho ...
written 3 months ago by
Manuel Landesfeind • 1.1k
0
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3
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424
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... @Asaf already mentioned that the topic is well-studied and I agree that little improvements will have little impact. In particular if you have to demonstrate economic impact in your proposal.
Industry likes de facto standards and well-established and often-used methods. I work in a CRO with all ki ...
written 10 months ago by
Manuel Landesfeind • 1.1k
0
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1
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993
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1
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... Thats interesting... for some reason I thought it would be hg38... don't know why.. ...
written 13 months ago by
Manuel Landesfeind • 1.1k
2
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1
answer
993
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1
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... What can be discussed is the threshold you use: when do you consider a variant as putative germline? 1%, 10%, ... allelic frequency? In any population or overall?
PS: If you figure out a good threshold or some literature, please share here because it will save me some time to evaluate this by mysel ...
written 14 months ago by
Manuel Landesfeind • 1.1k
1
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1
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993
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... I absolutely agree with Titus that gnomAD and ExAC are key databases. We use 1000G, HapMap and others because our established pipeline uses hg19 genome assembly.
Moving to hg38 and corresponding databases is in progress and I plan to use gnomAD and ExAC too. ...
written 14 months ago by
Manuel Landesfeind • 1.1k
0
votes
1
answer
993
views
1
answers
... For me the number of mutations in your tumors seems suspiciously high. We do a very similar approach in removing potential germline mutations from tumors lacking matched normal samples (using different annotation databases and no internal normal-pool).
In our models we usually retain between 500 an ...
written 14 months ago by
Manuel Landesfeind • 1.1k
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For Influence of RNA-seq read splitting on the BAQ calculation in samtools mpileup
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For C: Stop to make GUI with Java .... Use Qt 5 !!
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For C: Stop to make GUI with Java .... Use Qt 5 !!
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For A: Changing the header of a VCF file and the field correspondingly
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For A: Splice aware aligner - what does it mean?
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For A: Changing the header of a VCF file and the field correspondingly
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For A: Changing the header of a VCF file and the field correspondingly
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For C: Stop to make GUI with Java .... Use Qt 5 !!
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For C: How to deal with many uncharacterized protein in the blastx results?
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For C: How to deal with many uncharacterized protein in the blastx results?
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For C: Stop to make GUI with Java .... Use Qt 5 !!
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