estimate tumor purity from target capture sequencing

hi, everyone, is there a good way to estimate the tumor purity from target capture sequencing?i need to calculate the copy number and without the purity, the CN may be not accurate. thanks for your kind help.

tumor purity target capture sequencing estimation

• 2,313 views • link

updated 7.0 years ago by dariober

• written 7.0 years ago by lffu_0032

1 answer

The facets package detects copy number variants and gives you the purity and ploidy estimates.

If interested, I also wrote a wrapper to run the analysis as a single line command, see cnv_facets.

• 0 views • link

written 7.0 years ago by dariober

thank you. i see that the facet is suit for tumor-normal pair calling, but i have only tumor-only capture data...

• 0 views • link

written 6.7 years ago by lffu_0032

More posts like this

Reference Panel for Copy Number Analysis Based on Clinical Target Capture Sequencing
written 3.2 years ago by Noushin N

Hi everyone, I am starting on a project that involves somatic copy number analysis of tumor tissue profiled by clinical grade target capture sequencing (FoundationOne). …
No baf, cn1 and cn2 columns in cnvkit call output using vcf files
written 3.8 years ago by rahel14350 •

Dear all, I need to get major and minor cn values on some TSO500 tumor samples and one pooled Normal sample to calculate ccf, thus, …
tool for calculate tumor-only sample purity of wgs or wes
written 5.7 years ago by linouhao •

hi, is there a tool to calculate tumor only samle purity of wgs or wes? thanks a lot
Vst estimation across different populations from copy number data
written 5.9 years ago by rthapa •

Hi, I want to estimate Vst value across different population based on the copy number data. I have 5 populations and in each population, I …
copy number became inaccurate when downsampling different number fastq reads from a whole fastq file
written 6.5 years ago by lffu_0032

Hi, everyone: Recent i am doing CNV analysis, i find a strange thing: 1.when using whole data (after removed dup, for tumor and its control), …
estimate tumor purity from capture panel data using tumor-only mode
written 6.7 years ago by lffu_0032

Hi, everyone, i have a question: i want to call CNV from FFPE tumor using capture panel data, I need to estimate the tumor purity …
Whole Exome Sequencing Depth
written 7.8 years ago by bioinfonerd •

Hi, I want to calculate Copy number variations(CNV) from Whole exome seq data. What is the correct sequencing depth that can result in correct identification …
minus integer copy number when using --purity for cnvkit
written 8.1 years ago by xiaoqiaoliu •

Dear all, i tried to use estimated purity to adjust the allele specific copy number output from cnvkit, but it would generate minus copy number …
I need help with how to modify the sbdry parameter in DNAcopy
written 9.9 years ago by mikki •

My group has used VarScan and DNAcopy for CNV analysis from Whole Exome Sequencing data, where the tumor sample was taken from FFPE. We are …
Jointly Detect Somatic Copy Number Variations
written 12.5 years ago by lyz10302012

<p>Hi,</p> <p>Is there any good tools to jointly detect somatic copy number variations (like some tools for SNVs) from tumor-normal paired sequencing data? If not, …