User: Manuel Landesfeind
Manuel Landesfeind • 1.1k
- Reputation:
- 1,080
- Status:
- Trusted
- Location:
- Freiburg, Germany
- Last seen:
- 14 hours ago
- Joined:
- 2 years, 2 months ago
- Email:
- l**********@gmail.com
Posts by Manuel Landesfeind
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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 17 days ago by
Manuel Landesfeind • 1.1k
0
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1
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336
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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 3 months ago by
Manuel Landesfeind • 1.1k
2
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1
answer
336
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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 4 months ago by
Manuel Landesfeind • 1.1k
1
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1
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336
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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 4 months ago by
Manuel Landesfeind • 1.1k
0
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1
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336
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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 4 months ago by
Manuel Landesfeind • 1.1k
0
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2
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226
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2
answers
... 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 5 months ago by
Manuel Landesfeind • 1.1k
0
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2
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226
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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 5 months ago by
Manuel Landesfeind • 1.1k
0
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2
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226
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2
answers
... 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 5 months ago by
Manuel Landesfeind • 1.1k
2
votes
2
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232
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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 5 months ago by
Manuel Landesfeind • 1.1k
1
vote
2
answers
232
views
2
answers
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 5 months ago by
Manuel Landesfeind • 1.1k
Latest awards to Manuel Landesfeind
Appreciated
17 days ago,
created a post with more than 5 votes.
For C: Stop to make GUI with Java .... Use Qt 5 !!
Appreciated
3 months ago,
created a post with more than 5 votes.
For C: Stop to make GUI with Java .... Use Qt 5 !!
Guru
5 months ago,
received more than 100 upvotes.
Centurion
6 months ago,
created 100 posts.
Scholar
11 months ago,
created an answer that has been accepted.
For A: Changing the header of a VCF file and the field correspondingly
Good Answer
13 months ago,
created an answer that was upvoted at least 5 times.
For A: Splice aware aligner - what does it mean?
Scholar
15 months ago,
created an answer that has been accepted.
For A: Changing the header of a VCF file and the field correspondingly
Scholar
15 months ago,
created an answer that has been accepted.
For A: Changing the header of a VCF file and the field correspondingly
Appreciated
19 months ago,
created a post with more than 5 votes.
For C: Stop to make GUI with Java .... Use Qt 5 !!
Scholar
19 months ago,
created an answer that has been accepted.
For A: Changing the header of a VCF file and the field correspondingly
Voter
19 months ago,
voted more than 100 times.
Commentator
20 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
20 months ago,
created an answer that has been accepted.
For A: Changing the header of a VCF file and the field correspondingly
Commentator
21 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
22 months ago,
created a post with more than 5 votes.
For C: Stop to make GUI with Java .... Use Qt 5 !!
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
23 months 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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