User: Bogdan

gravatar for Bogdan
Bogdan480
Reputation:
480
Status:
Trusted
Location:
Palo Alto, CA, USA
Scholar ID:
Google Scholar Page
Last seen:
1 week ago
Joined:
5 years, 10 months ago
Email:
t*****@gmail.com

about me

Posts by Bogdan

<prev • 181 results • page 1 of 19 • next >
0
votes
1
answer
170
views
1
answers
Comment: C: filtering a VCF file based on genotype
... Thank you Ram for your help. Yes, i've used the "Rscript" calls from a shell script. ...
written 7 days ago by Bogdan480
0
votes
1
answer
170
views
1
answers
Comment: C: filtering a VCF file based on genotype
... Thank you Jorge. Yes, at the end, I have done it with BCFTOOlS: bcftools view --genotype ^miss $FILE > "${FILE%.vcf}.fGT.vcf" I was hoping to do everything in R, as it would be easier to assemble the entire pipeline in R (than to assemble all the scripts I have in a master bash shell .sh ...
written 8 days ago by Bogdan480 • updated 7 days ago by Ram15k
1
vote
1
answer
170
views
1
answers
Comment: A: filtering a VCF file based on genotype
... Dear gentlemen, thank you for your replies and help. Here I am posting the R code that I am using to do the filtering of a VCF file that is generated by DELLY and contains INVERSIONs only .. Any suggestions on how to post/link the input VCF file would be welcome. Thank you very much ! library ...
written 8 days ago by Bogdan480
4
votes
1
answer
170
views
5 follow
1
answer
filtering a VCF file based on genotype
... Dear all, I would appreciate having a piece of advice : how shall I filter a VCF file in order to exclude the GERMLINE and TUMOR samples that have a GENOTYPE of "./". in R/BioC, for example, if we aim to see the GENOTYPES in the vcf file, we receive the following messages : > geno(vcf)$GT[ ...
vcf written 8 days ago by Bogdan480 • updated 7 days ago by Ram15k
0
votes
1
answer
139
views
1
answers
Comment: C: 4C interaction analysis
... Thank you very much for your suggestions ! ...
written 18 days ago by Bogdan480
0
votes
0
answers
82
views
0
answers
Comment: C: normalization when calling CNV areas on a genome-wide scale in tumor-germline sa
... Thank you Chris for your gracious help .. ...
written 26 days ago by Bogdan480
0
votes
0
answers
82
views
0
answers
Comment: C: normalization when calling CNV areas on a genome-wide scale in tumor-germline sa
... Dear Chris, thank you for your suggestions. I would be very glad to use copyCat . A question though : I have seen distinct packages doing 1) global (genome-wide) normalization or 2) local (chromosome-wide) normalization ? Would you recommend to use 1) or 2) or perhaps I shall use both normalizat ...
written 27 days ago by Bogdan480
0
votes
0
answers
82
views
0
answers
normalization when calling CNV areas on a genome-wide scale in tumor-germline samples
... Dear all, please would you advise : what is a more reliable method for normalization when calling CNV areas on a genome-wide scale on tumor-germline paired samples ? And : shall we apply the normalization on a chromosome basis, or on a whole-genome ? Thanks a lot ! -- bogdan ...
cnv written 27 days ago by Bogdan480
0
votes
2
answers
200
views
2
answers
Comment: C: a realiable algorithm that calls INDELS of length 50bp-300bp in cancer genomes
... thank you Eric. good to hear from you ! please would you have any comments about DELLY, how well it does to call the INDELs in 30-300 bp range ? thanks. ...
written 8 weeks ago by Bogdan480
0
votes
2
answers
200
views
2
answers
Comment: C: a realiable algorithm that calls INDELS of length 50bp-300bp in cancer genomes
... thanks a lot Kevin ! may I add, have you used it extensively ? does it require a lot of filtering of the VCF files in order to get the reliable variants ? ...
written 9 weeks ago by Bogdan480

Latest awards to Bogdan

Popular Question 8 weeks ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 8 weeks ago, created a question with more than 1,000 views. For running GATK or Mutect or a somatic variant caller individual chromosomes
Popular Question 8 weeks ago, created a question with more than 1,000 views. For "for loop" and AUTOPLOT function
Popular Question 8 weeks ago, created a question with more than 1,000 views. For estimating tumor purity and ploidy and CNV
Popular Question 10 weeks ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 3 months ago, created a question with more than 1,000 views. For about merging VCF files
Student 3 months ago, asked a question with at least 3 up-votes. For filtering the somatic variants
Popular Question 3 months ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 5 months ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 6 months ago, created a question with more than 1,000 views. For about merging VCF files
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to analyze RIP-seq data
Student 6 months ago, asked a question with at least 3 up-votes. For filtering the somatic variants
Popular Question 8 months ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 10 months ago, created a question with more than 1,000 views. For intersect VCF files
Popular Question 11 months ago, created a question with more than 1,000 views. For about xlim() in ggbio and CIRCLE layout
Centurion 13 months ago, created 100 posts.
Student 13 months ago, asked a question with at least 3 up-votes. For annotation of SV (Structural Variants)
Supporter 14 months ago, voted at least 25 times.
Popular Question 23 months ago, created a question with more than 1,000 views. For about GRAnges and append
Scholar 2.1 years ago, created an answer that has been accepted. For A: Calculating fold change at enhancers and promoters

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1644 users visited in the last hour