SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 40
Search took 0.00 seconds.
Search: Posts Made By: vd4mindia
Forum: Bioinformatics 04-02-2015, 06:17 AM
Replies: 7
Views: 7,439
Posted By vd4mindia
No I have already figured out a tool that works...

No I have already figured out a tool that works best for this.. the bedops tool has a function vcf2bed works fit to convert the scenario and I already performed that and also am familiar with awk as...
Forum: Bioinformatics 04-01-2015, 06:46 AM
Replies: 7
Views: 7,439
Posted By vd4mindia
@inesdesantiago I have a situation where I have...

@inesdesantiago
I have a situation where I have output of SNPs from VarScan. I see the varscan outputs LOH( both as SNP and INDELS LOH). Now for INDELS its fairly easy to make a bed format file. But...
Forum: Bioinformatics 03-26-2015, 07:01 AM
Replies: 10
Views: 20,612
Posted By vd4mindia
Thank you very much for the reply. That makes...

Thank you very much for the reply. That makes sense.
Forum: Bioinformatics 03-25-2015, 10:43 AM
Replies: 10
Views: 20,612
Posted By vd4mindia
I would just want to ask you in case you have...

I would just want to ask you in case you have have not other bases as 0 in normal in that case do you still calculate the variant allele frequency as the above? Variant allele frequency should be...
Forum: Bioinformatics 03-09-2015, 03:34 AM
Replies: 0
Views: 1,386
Posted By vd4mindia
Unhappy Problem with Pindel output

Hi,

I have been using normal/tumor GATK processed realigned and recalibrate bam files for mutation , indel and CNV analysis. I have used this bam with VarScan, GATK, Lofreq, Mutect and I have...
Forum: Bioinformatics 02-09-2015, 04:53 AM
Replies: 0
Views: 1,322
Posted By vd4mindia
Using Phylosub for Inferring clonality

Hi,

I have recently come across a paper which developed a software phylosub with which one can infer the clonal heterogenity in both single sample tumors or more samples. I have WES data of ...
Forum: Literature Watch 02-05-2015, 01:34 AM
Replies: 77
Views: 50,361
Posted By vd4mindia
what should be the parameter for normal/tumor clone with varying coverage

I would like to discuss certain things with you regarding the samples am using to infer CNV with exome data with Control-FREEC. I am using WES tumor data. I have tumor sample with a coverage of...
Forum: Bioinformatics 01-27-2015, 05:45 AM
Replies: 3
Views: 1,939
Posted By vd4mindia
I have used VarScan2 on my data but does not give...

I have used VarScan2 on my data but does not give any inferring results, I have however had some sort of success with Control-FREEC, now am trying other tools that are useful in calling somatic CNV...
Forum: Bioinformatics 01-27-2015, 05:16 AM
Replies: 11
Views: 5,385
Posted By vd4mindia
am using the GATK DepthofCoverage output for...

am using the GATK DepthofCoverage output for exomeCNV, but am getting some error in dataframe.
My commands for normal and tumor for 3 chromosomes
chr.list = c("chr19","chr20","chr21")
normal =...
Forum: Bioinformatics 01-27-2015, 02:13 AM
Replies: 3
Views: 1,939
Posted By vd4mindia
@mrfox Did you find a workaround for this? I...

@mrfox

Did you find a workaround for this? I am also facing issues, am using ExomeCNV for first time, the bamcoverage.sh does not work well as they need old version of samtools, so I tried gatk...
Forum: Bioinformatics 01-26-2015, 08:48 AM
Replies: 11
Views: 5,385
Posted By vd4mindia
@spoonman I would like to know how to make...

@spoonman

I would like to know how to make the files read if I take the output of GATK depthofcoverage, since it contains one file that contains all the chromosome summary together. How do I use...
Forum: Bioinformatics 11-19-2014, 01:41 AM
Replies: 4
Views: 3,883
Posted By vd4mindia
Filtering varscan variants

I would like to ask removing the snps closer to indels at 1bp thus removes a lot of snps for me. But it is not a test for false positive right? I believe if am using the local realignment around...
Forum: Bioinformatics 11-18-2014, 05:28 AM
Replies: 2
Views: 1,847
Posted By vd4mindia
I also have a same question, I have also ran...

I also have a same question,

I have also ran the VarScan2 on my normal/tumor pair with p-value as 0.1 somatic p-value 0.001 and then ran the somatic filter with parameters -min-strands2 2...
Forum: Bioinformatics 09-03-2014, 04:18 AM
Replies: 10
Views: 20,612
Posted By vd4mindia
@lethalfang `Would you like to share the...

@lethalfang
`Would you like to share the pipeline for finding somatic mutations. I have 2 samples, one low and one high grade tumor and its normal. I want to detect the point somatic mutations. I...
Forum: Literature Watch 07-14-2014, 03:48 AM
Replies: 77
Views: 50,361
Posted By vd4mindia
Dear Velntina, Please find the output for...

Dear Velntina,

Please find the output for the above call, I have made 6 such calls but all had the same problem. Below am attaching the log of the output run and at what stage I get the...
Forum: Literature Watch 07-14-2014, 02:37 AM
Replies: 77
Views: 50,361
Posted By vd4mindia
Hi , I am using control-FREEC with exome...

Hi ,

I am using control-FREEC with exome sequencing data, so far I have been successful in implementing it on my normal control tumor pairs for CNA detection. I am now curious to apply it further...
Forum: Bioinformatics 10-18-2013, 02:32 AM
Replies: 9
Views: 19,858
Posted By vd4mindia
Yes I have queued a script and its still running....

Yes I have queued a script and its still running. Since am working from home my intenet is a bit weak so have to run script in cluster and cant asses the command line script so I was asking but it...
Forum: Bioinformatics 10-18-2013, 01:55 AM
Replies: 9
Views: 19,858
Posted By vd4mindia
I need some suggestion about the mark duplicates...

I need some suggestion about the mark duplicates command using picard tool, can anyone tell me if in the input and out label we can specify path as well or not? as I want to run 6 samples together so...
Forum: Bioinformatics 10-09-2013, 03:34 AM
Replies: 18
Views: 15,702
Posted By vd4mindia
@choishingwan I guess then I can use the...

@choishingwan

I guess then I can use the option of TableRecalibration, I am yet to run it , if it produces a bam file good enough else I will use the print read option which will surely produce a...
Forum: Bioinformatics 10-09-2013, 02:40 AM
Replies: 18
Views: 15,702
Posted By vd4mindia
@choishingwan , Thanks for your prompt...

@choishingwan ,

Thanks for your prompt reply. I would like to tell you that I am using the version 2.3 not the 2.7 one so is it wrong to use the DBSNP_137.vcf file with that? I hope this should...
Forum: Bioinformatics 10-09-2013, 02:31 AM
Replies: 18
Views: 15,702
Posted By vd4mindia
@thedamain, I need some information about...

@thedamain,

I need some information about the exomes.bed file which you are using. I see that most of the pipelines say that they generate it from the UCSC genome browser to restrict the output...
Forum: Bioinformatics 10-09-2013, 02:02 AM
Replies: 18
Views: 15,702
Posted By vd4mindia
Yes @choishingwan I checked and the fixmate step...

Yes @choishingwan I checked and the fixmate step is retired and am not using it but I have another query in the above line please let me know and share your views
Forum: Bioinformatics 10-09-2013, 01:59 AM
Replies: 18
Views: 15,702
Posted By vd4mindia
@thedamian, Yes I fixed it , I indexed it...

@thedamian,

Yes I fixed it , I indexed it again and then made the call and the local realignment step is running now. But i need some inputs for the base quality recalibration step. In the above...
Forum: Bioinformatics 10-09-2013, 12:47 AM
Replies: 18
Views: 15,702
Posted By vd4mindia
Hi I am facing some problems with the Local...

Hi I am facing some problems with the Local realignment step around the indels, I am using the marked bam file after the PCR duplicate marking step but I am getting the following error
##### ERROR...
Forum: Bioinformatics 10-07-2013, 11:47 AM
Replies: 18
Views: 15,702
Posted By vd4mindia
"The exome intervals I've gained using UCSC Table...

"The exome intervals I've gained using UCSC Table Browser http://genome.ucsc.edu/cgi-bin/hgTables?command=start"
Can you tell me how to get the exome intervals as you have referred
Showing results 1 to 25 of 40

 


All times are GMT -8. The time now is 02:24 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO