[silverfish]

Hi,

I am a beginner, and I just downloaded and tried CONTRA before using it on my samples. I first ran the test files provided. It worked paritally until it came to the reference file part and it says:

Error: The requested fasta database file (human_g1k_v37.fasta) could not be opened. Exiting!
Creating VCF file ...
ContraTest/sampleName/table/CNATable.10rd.10bases.20bins.vcf created.
Done...

The /Table/CNATable.10rd.10bases.20bins.txt is 1.9 MB in size. The CNATable.10rd.10bases.20bins.DetailsFILTERED.txt has just the headings. The VCF file is also empty with just the headers.

I re-downloaded the fasta file and still the same error. Can someone pl. help address this? the created vcf file, ofcourse is empty.

Thanks,

Thane

[shruti]

ADTex

Hi I am using ADTEx (1.0.4) but it is not running properly.
I always encounter either of the problems.
All my coordinates are in chr format for BAM, target etc files.

1.
Analysing CNV...
[1] "Analysing tumour sample with base ploidy : 3"
[1] "Analysing tumour sample with base ploidy : 2"
[1] "Analysing tumour sample with base ploidy : 4"
Error in CNA(baf$mirrored_BAF[baf$chrom == i], baf$chrom[baf$chrom == :
genomdat must be numeric
Execution halted
Error in CNA(baf$mirrored_BAF[baf$chrom == i], baf$chrom[baf$chrom == :
genomdat must be numeric
Execution halted
Error in file(file, "rt") : cannot open the connection
Calls: read_file -> read.delim -> read.table -> file
In addition: Warning message:

2.
Analysing CNV...
[1] "Analysing tumour sample with base ploidy : 2"
[1][1] "Analysing tumour sample with base ploidy : 3" "Analysing tumour sample with base ploidy : 4"

Error in dnorm(x, mean, sd, log) :
Non-numeric argument to mathematical function
Calls: predict.cnv -> viterbi -> dnorm
Execution halted
Error in dnorm(x, mean, sd, log) :
Non-numeric argument to mathematical function
Calls: predict.cnv -> viterbi -> dnorm
Execution halted
Error in dnorm(x, mean, sd, log) :
Non-numeric argument to mathematical function
Calls: predict.cnv -> viterbi -> dnorm
Execution halted
Error in file(file, "rt") : cannot open the connection
Calls: read_file -> read.delim -> read.table -> file

Have any of you encountered such a problem.

Thanks

shruti

[pmint]

Error in CNA(baf$mirrored_BAF[baf$chrom == i], baf$chrom[baf$chrom == :
genomdat must be numeric

I had same problem, and I solved.
It can be solved by adding 'mirrored_BAF' column in .baf file.
I added these command in the 147th line of cnv_analyse.R

tmp = baf$tumor_BAF
tmp[tmp > 0.5] = 1 - tmp[tmp > 0.5]
baf$mirrored_BAF = tmp

These are not so pretty, but I got results.

[Dataman]

ADTEx is the improved version of CoNVEx

http://adtex.sourceforge.net

cheers
jason

Hi All and Jason,

I am using ADTEx to perform copy number analysis of some exome sequencing data. ADTEx requires a B-allele frequency file in order to perform ploidy estimation and genotype prediction. However, I do not know how to create such file and the ADTEx tutorial does not explain it either. I was wondering if there is a general way to create B-allele frequency files that I do not know of!

The file as is explained in the tutorial should have the following fields:

chrom - chromosome name (same format as in BED or BAM file)
SNP_loc - location of the SNP
control_BAF - B allele frequency (BAF) at each SNP in control sample
tumor_BAF - B allele frequency (BAF) at each SNP in tumor sample
control_doc - Total read count at each SNP in control sample
tumor_doc - Total read count at each SNP in tumour sample

Thank you in advance for your responses and wishing you all a nice summer.