[svural]

Here is a good paper discussioning the tools
Comparative Studies of Copy Number Variation Detection Methods for Next-Generation Sequencing Technologies

[Alberto Magi]

Hi All,

if you want to make CNV/CNA detection by using whole-exome sequencing data try to use the new software package EXCAVATOR. The paper has beeen recently published on Genome Biology (http://genomebiology.com/2013/14/10/R120/abstract) and the package can be downloaded at http://sourceforge.net/projects/excavatortool/.
The EXCAVATOR package combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomic regions into five copy number states (two-copies deletion, single-copy deletion, neutral, three-copies and multiple-copies). EXCAVATOR is a suitable tool for the investiga- tion of CNVs in large-scale projects (such as the 1000 Genomes Project and the Cancer Genome Atlas) as well as in clinical research and diagnostic activities. EXCAVATOR has been tested on the analysis of healthy individuals sequenced by the 1000 Genomes Project consortium and on the analysis of cancer samples and has been compared with other three state of the art methods (ExomeCNV, CoNIFER and XHMM).
All the comparative analyses we performed highlighted the versatility of our software and its capability of overcoming the limits and drawbacks of currently available state of the art tools.

Alberto

[dGho]

EXCAVATOR documentation

Hi Alberto,

Where can I access documentation for how to run Excavator and the specifications of input and output files?

[shruti]

Hi Alberto,

I am running EXCAVATOR but I am always encountering the error

Error in JointSegIn(DataSeq1, muk, mi, smu, sepsilon, Pos1, omega, eta, :
NA/NaN/Inf in foreign function call (arg 2)
Calls: JointSegIn -> .Fortran
Execution halted

I would be grateful if you could help me with the error.

Thanks

Shruti

[ffavero]

Sequenza allele specific copy number

If you have paired normal/tumor samples you could try sequenza:

http://cbs.dtu.dk/biotools/sequenza/

Is written in python and R, is available from CRAN

It works for exome and wgs and is able to provide total and allele specific copy number, calculate tumor purity and ploidy.


Manuscript is in review, but the package is complete with extensive documentations and examples data.

[dickie_ho]

Just to back Alberto

EXCAVATOR is the best package i have came across for exome-seq data.

It has cross validated with my SNP array data and has even detected CNVs that the arrays did not detect that were actually functional when overlapped with RNA-seq and smallRNA-seq data

[swiri021]

Recently, I was faced that problem as same.

And I fixed the code in EXCAVATORInference.R at the lib/R/ folder

Look into that file.

you can see the variable 'Gene'

and go to the line of
DataSeg <- SegResults(seqChrom,TotalPredBreak,start,end,gene)

Can you see that ??? 'gene'

Just fix that as 'Gene'

I hope you run it well .

[swiri021]

Hi, shruti,

Recently, I was faced that problem as same.

And I fixed the code in EXCAVATORInference.R at the lib/R/ folder

Look into that file.

you can see the variable 'Gene'

and go to the line of
DataSeg <- SegResults(seqChrom,TotalPredBreak,start,end,gene)

Can you see that ??? 'gene'

Just fix that as 'Gene'

I hope you run it well .

[daghrach]

Hi swiri021 ,
I changed "gene" by "Gene" in EXCAVATORInference.R
DataSeg <- SegResults(seqChrom,TotalPredBreak,start,end,Gene)
But i'm having the same error when running the somatic mode .

[shruti]

Hi,

I was able to run EXCAVATOR successfully after these modifications with the help of Alberto.

Removed the chrY for the female samples and replacing line 151 in the EXCAVATORInference.R script:

seqChrom <- rbind(filterOut(seqChrom, smooth.region,outlier.SD.scale,smooth.SD.scale,trim))

with:

seqChrom <- rbind(seqChrom)


Hope it helps..

[Fatima.Z]

Error in JointSegIn

Hi Shruti,

I am running EXCAVATOR but at the end of the run I have this error:

Error in JointSegIn(DataSeq1, muk, mi, smu, sepsilon, Pos1, omega, eta, :
NA/NaN/Inf in foreign function call (arg 2)
Calls: JointSegIn -> .Fortran
Execution halted

I saw that you were encountering this error as well.
I modified the EXCAVATORInference.R script as you said but I have still the error.
Do you have any other suggestion for me?

[Fatima.Z]

Hi Shruti,

I am running EXCAVATOR but at the end of the run I have this error:

Error in JointSegIn(DataSeq1, muk, mi, smu, sepsilon, Pos1, omega, eta, :
NA/NaN/Inf in foreign function call (arg 3)
Calls: JointSegIn -> .Fortran
Execution halted

I saw that you were encountering this error as well.
I modified the EXCAVATORInference.R script as you said but I have still the error.
Do you have any other suggestion for me?