GISTIC2 using targeted panel sequencing data?

Hi, I have several targeted panel sequencing data. I got segmented log2 ratios and seg files using CNVkit. I would like to check driver events using GISTIC2. Can I use CNV data from targeted sequencing instead of WES or WGS as an GISTIC2 input? Thanks.

targeted sequencing cnv

• 1,253 views • link

written 7.3 years ago by luna •

0 answers

No answers yet.

More posts like this

Merging segment CNV files
written 1.0 years ago by avelarbio46 •

Hello all I have called somatic CNVs with both CNVkit (short-reads) and SAVANA (long-read) for paired tumor samples. This means I have the segment data …
Apply BSQR for Targeted Sequencing
written 2.7 years ago by Manuel Sokolov Ravasqueira •

Hi! I am performing variant calling starting from a fasta resulting targeted sequencing of ~320 cancer genes, I followed the GATK best practices aligning with …
CNVkit detected CNV number
written 5.3 years ago by enes •

Hi, I am newbie in CNVKit I want to analyse clinical exome panel sample in CNVkit to detect copy number variants. When I tried with …
CNV analysis pipeline using Gistic2
written 6.6 years ago by samane. •

Dear every body, I downloaded level 3 CNV data from TCGA (segmented files). I am going to use Gistic2 to identify recurrent CNVs ? There …
It's there any GISTIC2.0 like tools?
written 6.8 years ago by MatthewP

Hello, I re-edit this question, orginal question: `GISTIC2.0` can find CNV across a set of samples. I want to know it's there other tools can …
Gistic input error : No copy number data detected
written 8.7 years ago by mm.beauty.lin •

Hello everyone, I am using GISTIC version 2.0.23 to analyse CNVs of nasopharyngeal carcinoma, and I get the CNVs of WGS and WES data by …
How to import the output of CNVkit into GISTIC2.0 ?
written 8.9 years ago by Tonny •

Hi, I get the many CNV results from sing cell genome sequencing with CNVkit. I'd like to get the driver CNV with GISTIC2.0. I have …
Is there any method for using WES data from Illumina Hiseq into ABSOLUTE?
written 9.0 years ago by namhaesly •

Hi I'm a new to bioinformatics. I have a task to analyze WES data using ABSOLUTE R package. I must use ABSOLUTE for that task …
The ABSOLUTE input and HAPSEG output format
written 9.4 years ago by shiyang93 •

HI I want to use the ABSOLUTE to analyze my WES data. I have already segmented my data, with log2 ratio of both allele(log2-allele1, log2-allele2, …
Help with understanding CNVkit output
written 10.5 years ago by alons

Hi all, I need some help with understanding the output of CNVkit, specifically Segmented log2 ratios (.cns) and the exported CNVs in VCF format. I'm …