User: Eric T.

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Eric T.2.3k
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http://etalog.blogspot...
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etalevich
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Bioinformatics at UCSF's Clinical Cancer Genomics Lab.

Posts by Eric T.

<prev • 217 results • page 1 of 22 • next >
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Answer: A: Running cnvkit batch with -y parameter
... If you use `-y` anywhere, you have to use it everywhere. Did the `diagram` plot come from the same `batch` run where `-y` was used? If not, you can just run `diagram` again and add `-y`. Full details here: https://cnvkit.readthedocs.io/en/stable/sex.html ...
written 22 days ago by Eric T.2.3k
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Answer: A: Best variant caller for CNVkit
... For SNVs, any variant caller that will do joint genotyping of the tumor and normal samples without dropping germline variants is fine. VarDict is good, and FreeBayes is fine too. Mutect2 unfortunately drops the germline variants, which CNVkit needs for LOH detection. See here: https://cnvkit.readthe ...
written 6 weeks ago by Eric T.2.3k
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Comment: C: CNVkit: gene results not in output
... OK, so far I see no reason for it to disappear. Can you track down the step in the pipeline where the gene disappears? - Are those bins actually labeled as "CCNE2" in your reference.cnn file? - After `fix`, is the CCNE2 in the output .cnr file? Are those bins (same coordinates as in the .cnn) pres ...
written 9 weeks ago by Eric T.2.3k
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Answer: A: CNVkit: gene results not in output
... I'm not quite sure what's happening in your data, but to clarify: - How did you run CNVkit, and which version did you use? - Does the gene name appear in the .cns file? Is it in a short segment by itself, or included in a segment with other genes on it? - Does the gene appear in the reference .cnn ...
written 11 weeks ago by Eric T.2.3k
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Answer: A: minus integer copy number when using --purity for cnvkit
... You are right that the `cn` and `cn2` values there should be 0, not -1. It's a quirk of rounding -- you can interpret -1 the same as 0, meaning full deletion. I thought I'd squashed this behavior in recent versions of CNVkit. Are you using the latest version, 0.9.3? ...
written 3 months ago by Eric T.2.3k
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Answer: A: Using CNVkit to identify poor-quality normal samples
... 1. You can run the `metrics` command with any .cnn or .cnr file, so just run it with the targetcoverage.cnn and antitargetcoverage.cnn files as you would with a .cnr file. Segments are not needed. 2. I suggest looking at the "stdev" or "bivar" column, depending on whether the presence of outliers o ...
written 4 months ago by Eric T.2.3k
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Answer: A: Is there a way to plot both tumor and normal samples' copy number segments on t
... 1. This feature isn't available on the command line, currently. It would be a nice feature, and you're not the first to request it. I've opened a ticket for it here: https://github.com/etal/cnvkit/issues/353 However, within the Python interpreter or in a script you can use `cnvlib.do_scatter` to ge ...
written 4 months ago by Eric T.2.3k
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Comment: C: CNV details about the normal samples?
... Yes, you can run the rest of the pipeline with the control samples' targetcoverage.cnn and antitargetcoverage.cnn files versus the existing reference.cnn file, as if the controls were additional test samples. The rest of the pipeline is the same after you've run the `fix` command. Or, if you don't ...
written 4 months ago by Eric T.2.3k
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Answer: A: a realiable algorithm that calls INDELS of length 50bp-300bp in cancer genomes
... LUMPY and Manta do well in this range, provided you have sequencing coverage around the relevant breakpoints. ...
written 6 months ago by Eric T.2.3k
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Answer: A: CNV detection using BAM file
... Most read-depth-based CNV callers operate on sorted BAM files. For targeted amplicon sequencing, don't remove PCR duplicates. For WGS and hybrid capture, do remove duplicates. The authors of each method will usually describe exactly what you need to provide as input to their programs. ...
written 6 months ago by Eric T.2.3k

Latest awards to Eric T.

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 4 months ago, created an answer that has been accepted. For A: Local alignment in biopython
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 6 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Appreciated 6 months ago, created a post with more than 5 votes. For A: When Should We Develop Biopython That Support Python 3.X?
Scholar 8 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: When Should We Develop Biopython That Support Python 3.X?
Scholar 11 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 13 months ago, created an answer that has been accepted. For A: Local alignment in biopython
Scholar 13 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Scholar 14 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 17 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Scholar 18 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Regarding Pseudokinases
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Regarding Pseudokinases
Scholar 19 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Popular Question 21 months ago, created a question with more than 1,000 views. For CNVkit, robust genome-wide copy number detection from DNA sequencing
Appreciated 21 months ago, created a post with more than 5 votes. For A: When Should We Develop Biopython That Support Python 3.X?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Regarding Pseudokinases

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