User: Manuel Landesfeind
Manuel Landesfeind • 1.1k
- Reputation:
- 1,120
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- Location:
- Freiburg, Germany
- Last seen:
- 12 hours ago
- Joined:
- 2 years, 9 months ago
- Email:
- l**********@gmail.com
Posts by Manuel Landesfeind
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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 7 days ago by
Manuel Landesfeind • 1.1k
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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 7 days ago by
Manuel Landesfeind • 1.1k
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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 9 days ago by
Manuel Landesfeind • 1.1k
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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 7 months ago by
Manuel Landesfeind • 1.1k
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... Thats interesting... for some reason I thought it would be hg38... don't know why.. ...
written 11 months ago by
Manuel Landesfeind • 1.1k
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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 11 months ago by
Manuel Landesfeind • 1.1k
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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 11 months ago by
Manuel Landesfeind • 1.1k
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... 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 11 months ago by
Manuel Landesfeind • 1.1k
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452
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... What do you want to demonstrate with the study? If you are interested in the biological results (i.e., what are the mutations of your biological sample) I recommend combining on the BAM level. This will increase the total coverage and thus gives you a higher accuracy for variant detection. In partic ...
written 12 months ago by
Manuel Landesfeind • 1.1k
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... > ... I wasn't using a large bam file containing all of these libraries was that it was taking too much time to crunch
What does that mean? Can you lay out the details of the sequencing a little bit more?
How do these different libraries compare? Do you consider them technical replicates? Or wa ...
written 12 months ago by
Manuel Landesfeind • 1.1k
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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 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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