Tumor germline CNA caller- concensus

Hi all, I was wondering is the folks here might suggest a current consensus for CNA/ CNV detection in germline cancer samples from NGS studies.

The couple of tools I found are CNVKit and ascat, any more out there that I could look into or preferably a pipeline for that?

Thanks in advance.

cna cnv ngs

• 1,877 views • link

written 10.1 years ago by win

0 answers

No answers yet.

More posts like this

Tools for chromosomal aneuploidy detection
written 2.2 years ago by adarsh •

Hi, I am developing a pipeline for detection of chromosomal aneupoloidy detection based on single sample. I went through several CNV calling tools, but most …
Running ASCAT without matched normal sample
written 2.5 years ago by Riccardo •

Hello! I am trying to run ASCAT for Copy Number Analysis on tumour NGS-sequenced data. However, the samples do not have their matched normal. Is …
WES CNV analysis
written 2.9 years ago by Avinash •

Hi, I am new to CNV analysis and beginner in R language. I am trying to call germline CNVs using exome data using ExomeDepth. I …
how to calculate BAF and LRR from VCF or BCF files?
written 4.8 years ago by xiaoguang

Hi, Do anyone know how to calculate BAF(B-allele frequency) and log R ratio from SNP calling pipeline( bcftoools mpileup & call) ? I read some …
Popular CNV detection tools
written 6.9 years ago by Floydian_slip

Hi, I was wondering what are some of the popular CNV detection tools from NGS data? I am looking for ones that can also detect …
Detecting Dispersed vs tandem duplicated
written 7.0 years ago by znl207 •

I am working with CNVs in a population, I've used a couple of different detection methods, I am currently using lumpy and delly- I am …
CNVKit for cancer germline mutation detection
written 10.1 years ago by win

Hi all, I am planning to use CNVKit and haven't come across information that clearly states if CNVKit maybe used for germline cancer mutation detection. …
Annotation of Structural Variants and CNVs
written 10.4 years ago by alons

Hi all, We're performing NGS on cancer DNA samples with a custom panel of target regions in different genes. Our structural variants & CNV detection …
Tools for SV & CNV detection
written 10.5 years ago by alons

Hi all, We're performing NGS on cancer DNA samples with a custom panel of target regions in different genes. From your experience & knowledge, which …
Detect CNVs in single sample using cn.MOPS
written 10.6 years ago by win

<p>Hi all,</p> <p>Using cn.MOPS for CNV detection and it requires optimally 6 samples (6 BAM files) to effectively run the analysis. I am generating CNV …