User: Eric T.

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Eric T.2.1k
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Location:
San Francisco, CA
Website:
http://etalog.blogspot...
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etalevich
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Last seen:
1 week, 4 days ago
Joined:
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Bioinformatics at UCSF's Clinical Cancer Genomics Lab.

Posts by Eric T.

<prev • 211 results • page 1 of 22 • next >
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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 12 days ago by Eric T.2.1k
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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 12 days ago by Eric T.2.1k
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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 9 weeks ago by Eric T.2.1k
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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 9 weeks ago by Eric T.2.1k
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Answer: A: Detect exon deletion/duplication from NGS amplicon
... The approach you described is similar to what [CNVkit][1] does -- see the bundled script [cnv_ztest.py][2] for single-exon testing. There are other methods designed specifically for targeted amplicon sequencing that go beyond the above. For example, [OncoCNV][3] reportedly works well. [1]: http ...
written 9 weeks ago by Eric T.2.1k
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Answer: A: How to use DNAcopy package to analyze Affymetrix SNP array?
... You might have better luck with the [PSCBS][1] package, which wraps DNAcopy and includes more functionality (and documentation) for processing SNP data. [1]: https://github.com/HenrikBengtsson/PSCBS ...
written 11 weeks ago by Eric T.2.1k
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Answer: A: CNVkit segmetrics error
... Sorry for the trouble. This was a bug in the 0.9.2 release. I've released a new version 0.9.3 that includes a fix, so you can upgrade to get a functioning CNVkit installation. ...
written 11 weeks ago by Eric T.2.1k
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Answer: A: WGS coverage (depth) for CNV detection
... Yes, that's about right. The signal-to-noise ratio for read-depth-based CNV calling is related to the number of reads or bases per window. ...
written 11 weeks ago by Eric T.2.1k
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Comment: C: CNVkit : small CNV calling
... The `autobin` command will do this calculation for you, or you can see the source code (cnvlib.autobin) and [documentation][1] for that command to see how it's done. [1]: https://cnvkit.readthedocs.io/en/stable/pipeline.html#autobin ...
written 11 weeks ago by Eric T.2.1k
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Comment: C: Using THETA2 from CNVkit: what king of vcf do you need?
... You'd think so, but Mutect also tends to filter the germline variants even when you tell it not to, leaving relatively few SNPs that CNVkit can use for the BAF calculation. It's better to use HaplotypeCaller to get comprehensive germline SNP calls. ...
written 12 weeks ago by Eric T.2.1k

Latest awards to Eric T.

Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 10 weeks ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: When Should We Develop Biopython That Support Python 3.X?
Scholar 3 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Good Answer 7 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 7 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 9 months ago, created an answer that has been accepted. For A: Local alignment in biopython
Scholar 9 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
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
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
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Scholar 14 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: Regarding Pseudokinases
Popular Question 17 months ago, created a question with more than 1,000 views. For CNVkit, robust genome-wide copy number detection from DNA sequencing
Appreciated 17 months ago, created a post with more than 5 votes. For A: When Should We Develop Biopython That Support Python 3.X?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Regarding Pseudokinases
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Scholar 22 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Scholar 22 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data

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