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 • 219 results • page 1 of 22 • next >
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Answer: A: CNV calling from exome sequencing data with a low number of samples
... If you're looking for de novo CNVs in the proband, you can use CNVkit to build a reference from the two parent samples. The results will still be noisy, so see the "[calling][1]" and "[germline][2]" pages in the documentation for suggestions to clean up the results. [1]: https://cnvkit.readthedoc ...
written 5 weeks ago by Eric T.2.3k
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Comment: C: CNVkit for germline samples
... Thanks for catching this, I've updated the link above. It's now: https://github.com/etal/cnvkit/blob/master/scripts/cnv_ztest.py ...
written 6 weeks ago by Eric T.2.3k
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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 10 weeks 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 3 months 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 3 months 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 4 months 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 4 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 5 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 6 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 6 months ago by Eric T.2.3k

Latest awards to Eric T.

Popular Question 5 weeks ago, created a question with more than 1,000 views. For CNVkit, robust genome-wide copy number detection from DNA sequencing
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 5 months ago, created an answer that has been accepted. For A: Local alignment in biopython
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Appreciated 8 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
Scholar 9 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: When Should We Develop Biopython That Support Python 3.X?
Teacher 13 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: ABSOLUTE to estimate tumour purity from WES data
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 15 months ago, created an answer that has been accepted. For A: Local alignment in biopython
Scholar 15 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 15 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: Domain Search Using Hmmer
Scholar 19 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Regarding Pseudokinases
Scholar 20 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Scholar 20 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Regarding Pseudokinases
Popular Question 23 months ago, created a question with more than 1,000 views. For CNVkit, robust genome-wide copy number detection from DNA sequencing
Appreciated 23 months ago, created a post with more than 5 votes. For A: When Should We Develop Biopython That Support Python 3.X?

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