User: Bogdan

gravatar for Bogdan
Bogdan260
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260
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Trusted
Location:
Palo Alto, CA, USA
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1 week, 2 days ago
Joined:
5 years ago
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Posts by Bogdan

<prev • 106 results • page 1 of 11 • next >
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Comment: C: WES or WGS analysis of cancer samples with no matched germline
... Thanks Marcus ! yes, I am still using GATK 3.5, as we started with GATK 3.5 based pipeline a long time ago . If you do not mind, may I ask, what resource do you use for GATK4beta documentation ? thanks ! ...
written 10 days ago by Bogdan260
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Comment: C: WES or WGS analysis of cancer samples with no matched germline
... Dear Marcus, thank a lot for your suggestions. Yes, we have been using MUTECT2 and cn.MOPS for detecting SNV and CNV in germline-tumor pairs. However, when we have only a TUMOR sample (with no GERMLINE sequence), may I ask, how would you run MUTECT2 ? ...
written 10 days ago by Bogdan260
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Comment: C: WES or WGS analysis of cancer samples with no matched germline
... Hi Wouter, thanks : we aim to identify the SNV and CNV in the tumor samples (and some of these samples do not have a matched normal sample). ...
written 11 days ago by Bogdan260
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WES or WGS analysis of cancer samples with no matched germline
... Dear all, although this question has been asked before (~ 2 years ago), if I may ask it again, as I am looking for some updated workflows, strategies, ideas : "what would be the acceptable pipeline for processing WES or WGS data from primary tumors that do not have matched germlines sequences ?" ...
wgs wes snv cnv written 11 days ago by Bogdan260 • updated 11 days ago by markus.riester180
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about using cn.MOPS in detecting CNV in WES of germline-tumor samples
... Dear all, Please may I ask for an advice regarding the use of cn.MOPS BioC package (http://bioconductor.org/packages/release/bioc/html/cn.mops.html) on WES data containing TUMOR-GERMLINE paired samples. I wrote the following piece of R code (below) -- please would you let me know if it looks fine, ...
tumor cn.mops cnv written 6 weeks ago by Bogdan260
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Comment: C: extracting Allele Read Counts
... thank you Pierre for your suggestions. ...
written 3 months ago by Bogdan260
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extracting Allele Read Counts
... Dear all, please could you advise : given a (tumor) BAM file and a (germline) VCF file, what tool shall i use in order to extract the Allele Read Counts for each heterozygous SNP (from the vcf file) ? many thanks, -- bogdan ...
snp cnv titan written 3 months ago by Bogdan260 • updated 3 months ago by Pierre Lindenbaum96k
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Comment: C: annotation of SV (Structural Variants)
... ok ;) thank you, Ram ;) ...
written 4 months ago by Bogdan260
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Comment: C: annotation of SV (Structural Variants)
... thanks, Ram ;) a pretty exciting conversation, I shall say ;) ...
written 4 months ago by Bogdan260
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Comment: A: annotation of SV (Structural Variants)
... Dear Daniel, thank you for the information on SV calling. Considering your experience with all SV callers, and the nice ROC curves from your publication, may I ask please : -- about filtering, would you have please strong recommendation about the numerical values for Allele Fraction, number of PAI ...
written 4 months ago by Bogdan260

Latest awards to Bogdan

Popular Question 6 weeks ago, created a question with more than 1,000 views. For about xlim() in ggbio and CIRCLE layout
Centurion 3 months ago, created 100 posts.
Student 4 months ago, asked a question with at least 3 up-votes. For annotation of SV (Structural Variants)
Supporter 5 months ago, voted at least 25 times.
Popular Question 14 months ago, created a question with more than 1,000 views. For about GRAnges and append
Scholar 15 months ago, created an answer that has been accepted. For A: Calculating fold change at enhancers and promoters

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