SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Inferring absolute copy number by using NGS data molcov Bioinformatics 2 12-28-2014 10:47 PM
Inferring (visualizing) haplotypes Marius Bioinformatics 1 07-11-2014 04:33 AM

Reply
 
Thread Tools
Old 02-09-2015, 04:53 AM   #1
vd4mindia
Member
 
Location: Milan

Join Date: May 2013
Posts: 40
Default 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 single sample tumor with its matched control. I would like to use the software but I do not see if anyone used or not? I am unable to understand how to prepare the data.txt input file which is used to detect the clonality. There is something as mu_v and mu_r column which is needed to be created. I am not sure how to do it. If anyone has experience I would like to know more about the way to create the data file. How to also get the values of delta_r and delta_v. It would be nice if any test sample is provided on which I can try with a test protocol. In my case I have bam files also I have vcf from VarScan2 which I have used to generate the columns for data.txt but I need to know how to do it for the rest columns like mu_r , mv_r, delta_r and delta_v. I would like some suggestions

Regards
vd4mindia is offline   Reply With Quote
Reply

Tags
cnv, exome sequecing, ngs analysis

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:43 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO