User: alons

gravatar for alons
alons270
Reputation:
270
Status:
Trusted
Location:
Rehovot
Last seen:
8 months, 3 weeks ago
Joined:
4 years, 5 months ago
Email:
a****@genesort.com

Posts by alons

<prev • 50 results • page 1 of 5 • next >
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Comment: C: MAGERI: a software tool for calling rare variants and detecting circulating tumo
... Thank you very much Mikhail, we will look into it! ...
written 10 months ago by alons270
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Comment: A: MAGERI: a software tool for calling rare variants and detecting circulating tumo
... Hi Mikhail! We're trying to run MAGERI on one of our cloud machines. However, it seems to fail on memory. We're looking to upgrade the machine, what are the minimum and optimal system requirements for your software? Thank you very much in advance! Best, Alon ...
written 10 months ago by alons270
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Comment: C: annotation of SV (structural variants)
... I see, I'll try too, please update if you succeed. I will as well. ...
written 22 months ago by alons270
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Comment: C: annotation of SV (structural variants)
... Hi, how can you use Snpeff to annotate translocations for example? ...
written 22 months ago by alons270
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Comment: C: CNVKIT import errors
... Great! Thank you. Seems to be working now, running it. ...
written 22 months ago by alons270
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Comment: C: CNVKIT import errors
... I would but I think the developer of CNVkit (Eric T.) would want to see this first, get his input on it, might be a potential bug. He's pretty active in this forum. ...
written 22 months ago by alons270
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CNVKIT import errors
... Hi all, I'm trying to run CNVkit (from source, in linux) after following the [installation instructions][1] on the [github page][2] but running into import errors which seem to be rare as I couldn't find any references online: Traceback (most recent call last): File "cnvkit.py", line 8, ...
cnvkit python cnv linux written 22 months ago by alons270 • updated 22 months ago by Eric T.2.5k
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Variant calling step order question: base recalibration & mark duplicates, which is first?
... Hi all, We're going through & revising our variant calling pipeline on NGS data from cancer patients and a question came up: Which step should be done **first** (and why), **base recalibration** or **mark duplicates**? **Currently** we **recalibrate bases** first and then **mark duplicates** ...
variant calling ngs pipeline cancer written 2.3 years ago by alons270 • updated 2.3 years ago by Brian Bushnell17k
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Answer: A: Cancer CNV workflow
... We've started using CNVkit recently for our cancer CNV detection in NGS results workflow with good results: [CNVkit docs][1] It has both plots & text data and the documentation is pretty comprehensive. You can do tumor vs. normal or just tumor analysis. The author, Eric Talevich, is around this ...
written 3.5 years ago by alons270
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Freebayes tumor vs. normal inquiry
... HI all, I've been trying to run Freebayes variant caller on a pair of tumor-normal samples but I can't seem to get the bar column for the normal bam file or the tumor. The commands I tried were: freebayes -F 0.01 -C 2 --pooled-continuous --fasta-reference efgenome.fa tumor/aligned_sorted.bam ...
ngs tumor freebayes snp written 3.6 years ago by alons270 • updated 3.2 years ago by sambrightman20

Latest awards to alons

Student 10 months ago, asked a question with at least 3 up-votes. For Help with understanding CNVkit output
Popular Question 19 months ago, created a question with more than 1,000 views. For Databases and annotation of translocations
Scholar 19 months ago, created an answer that has been accepted. For A: Can I bulid a new reference for bwa ?
Popular Question 21 months ago, created a question with more than 1,000 views. For GATK recalibration, duplicates & realignment
Appreciated 3.4 years ago, created a post with more than 5 votes. For Annotation of Structural Variants and CNVs
Good Question 3.4 years ago, asked a question that was upvoted at least 5 times. For Annotation of Structural Variants and CNVs
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Lack of consensus between NGS & Sanger sequencing on indels/mutations
Popular Question 3.4 years ago, created a question with more than 1,000 views. For GATK recalibration, duplicates & realignment
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Tools for SV & CNV detection
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Filter/Annotate VCF with dbSNP during variant calling workflow
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Help with understanding CNVkit output
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Annotation of Structural Variants and CNVs
Scholar 3.7 years ago, created an answer that has been accepted. For A: Can I bulid a new reference for bwa ?
Student 3.7 years ago, asked a question with at least 3 up-votes. For Annotation of Structural Variants and CNVs
Supporter 3.8 years ago, voted at least 25 times.

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