User: Manuel Landesfeind

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1,100
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Location:
Freiburg, Germany
Last seen:
2 weeks, 6 days ago
Joined:
2 years, 4 months ago
Email:
l**********@gmail.com

Posts by Manuel Landesfeind

<prev • 112 results • page 1 of 12 • next >
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Answer: A: Another statistical model to estimate gene/transcript expression
... @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 weeks ago by Manuel Landesfeind1.1k
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Comment: C: Somatic Mutation Identification for Tumor without Normal
... Thats interesting... for some reason I thought it would be hg38... don't know why.. ...
written 5 months ago by Manuel Landesfeind1.1k
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Comment: C: Somatic Mutation Identification for Tumor without Normal
... 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 5 months ago by Manuel Landesfeind1.1k
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Comment: C: Somatic Mutation Identification for Tumor without Normal
... 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 5 months ago by Manuel Landesfeind1.1k
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Answer: A: Somatic Mutation Identification for Tumor without Normal
... 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 5 months ago by Manuel Landesfeind1.1k
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Comment: C: Variant calling from multiple sequencing runs for a single samples
... 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 6 months ago by Manuel Landesfeind1.1k
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Comment: C: Variant calling from multiple sequencing runs for a single samples
... > ... 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 6 months ago by Manuel Landesfeind1.1k
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Answer: A: Variant calling from multiple sequencing runs for a single samples
... From the INFO-field `DP4`, I deduce, that you have used samtools/bcftools for calling already? If yes, I recommend joint variant calling: bcftools mpileup --annotate 'FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP' $run_1_lib1.bam $run_1_lib2.bam [ ... and all other bam files you have] | bcftools ca ...
written 6 months ago by Manuel Landesfeind1.1k
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Comment: C: VCF file problem
... I have no idea - but i guess yes: they somehow inferred variants and used the major allele as reference. Probably, you should contact the people that created the VCF file to ask for the methods... Apart from that: without knowing the exact reference that was used (i.e., having the same FASTA file) ...
written 7 months ago by Manuel Landesfeind1.1k
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Comment: C: VCF file problem
... Your VCF file does not adhere to [the VCF specifications][1]. In a proper VCF, every template sequence (i.e., chromosome or contig) must be defined in the header, like exemplified in Section 1.1 of the specification (look for the line starting with `##contig= ...
written 7 months ago by Manuel Landesfeind1.1k

Latest awards to Manuel Landesfeind

Appreciated 10 weeks ago, created a post with more than 5 votes. For C: Stop to make GUI with Java .... Use Qt 5 !!
Appreciated 5 months ago, created a post with more than 5 votes. For C: Stop to make GUI with Java .... Use Qt 5 !!
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to cache reads?
Guru 7 months ago, received more than 100 upvotes.
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to cache reads?
Centurion 8 months ago, created 100 posts.
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How to cache reads?
Scholar 13 months ago, created an answer that has been accepted. For A: Changing the header of a VCF file and the field correspondingly
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How to cache reads?
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Splice aware aligner - what does it mean?
Scholar 17 months ago, created an answer that has been accepted. For A: Changing the header of a VCF file and the field correspondingly
Scholar 17 months ago, created an answer that has been accepted. For A: Changing the header of a VCF file and the field correspondingly
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How to cache reads?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How to cache reads?
Appreciated 21 months ago, created a post with more than 5 votes. For C: Stop to make GUI with Java .... Use Qt 5 !!
Scholar 21 months ago, created an answer that has been accepted. For A: Changing the header of a VCF file and the field correspondingly
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: How to cache reads?
Voter 21 months ago, voted more than 100 times.
Commentator 22 months ago, created a comment with at least 3 up-votes. For C: How to deal with many uncharacterized protein in the blastx results?
Scholar 22 months ago, created an answer that has been accepted. For A: Changing the header of a VCF file and the field correspondingly
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: How to cache reads?
Commentator 23 months ago, created a comment with at least 3 up-votes. For C: How to deal with many uncharacterized protein in the blastx results?
Appreciated 23 months ago, created a post with more than 5 votes. For C: Stop to make GUI with Java .... Use Qt 5 !!
Commentator 24 months ago, created a comment with at least 3 up-votes. For C: How to deal with many uncharacterized protein in the blastx results?
Scholar 2.1 years ago, created an answer that has been accepted. For A: Changing the header of a VCF file and the field correspondingly

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