Questions tagged [cnv]

Copy Number Variation. Questions about how to define, find, annotate, study CNVs. Algorithms.

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Creating msk file for Illumina Array Analysis CLI Copy number train

recently I'm researching on how to detect CNV from Illumina microarray data. I found that Illumina has Array Analysis CLI software for this task, and I need to train the CN model myself, since the ...
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1 vote
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open source tools for CNV analysis from illumina SNP array

What are the best open source tools to analyse copy number variation using Illumina SNP array data...preferably R based tools, but open to other languages as well. I'm working with leukemia sample and ...
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2 votes
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Assess ploidy estimation through SNV and CNV results

I want to assess ploidy estimation (i.e., diploid vs tetraploid) in a set of samples for which I have both results from the variant caller (i.e., SNVs) and from the copy number caller. What are the ...
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4 votes
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How to summarize multiple exon copy numbers into copy number of the corresponding gene

I have a matrix, sample by exon, containing a copy number value for each pair (sample, exon). I would like to generate a second matrix, sample by gene, where the copy number of the exons is ...
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1 vote
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Definition of "proband" in CNV analysis

I am reading this paper regarding de novo CNV analysis in Schizophrenia: Accordingly, such CNVs must frequently occur as recurrent de novo mutations. In a sample of 662 schizophrenia proband–parent ...
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1 vote
1 answer
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A unified database for CNV, SNP, Indel and MSI

I am looking for a database or different databases where I can find information on different gene variants for a gene. As an example if I enter PPARG, I could be able to see SNPs, CNV, InDels and MSI. ...
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1 answer
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polidy VCF file for Canvas somatic-wgs cnv calling

I am trying to run Illumina CANVAS cnv caller for Somatic-WGS. There is an option "--ploidy-vcf" which is mandatory to supply, but don't know what exactly that mean. I had supplied the CNV....
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2 votes
1 answer
34 views

Cromwell: can't find file ID

I am using Cromwell to test a CWL (common workflow language) implementation of the GATK somatic CNV (copy number variation) pipeline. I am currently getting the following error (full log at the end): ...
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1 answer
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How to visualise the proportion of clonal genes to sub clonal genes [duplicate]

I have a data frame ...
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-1 votes
2 answers
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Calculating the number of probes for a given genomic range

I have a big data frame like this for copy number (exome seq) ...
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1 vote
0 answers
31 views

Confusion about GISTIC threshold

Please, can you help me with a confusion? In whole genome sequencing, if Total copy number (major + minor allele copy number by SCAT R package) for SMAD4 in a ...
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1 answer
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Joining columns to a sorted file

I have had a segmentation file (copy number) like below ...
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1 vote
1 answer
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What does this statement mean?

I have a copy number segment file with this by SCAT R package ...
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2 votes
2 answers
62 views

Detection of CNV(InDel) of intermediate size

My impression is that small InDel (a couple of bp) is identified through cigar string in BAM and typical CNV (at least thousands of bp) is detected through read depth. What about InDel or CNV with ...
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1 answer
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Arm-level SCNA does not change mRNA expression level?

It is almost common sense that local amplification of gene increase the its mRNA expression . I recently heard that large scale SCNA (such as arm-level amplification) does not increase the mRNA ...
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2 votes
2 answers
43 views

Method to detect genome doubling

CNV is usually detected using either read depth or SNP VAF. However, neither of these methods can detect CNV in case of genome doubling (assuming genome doubling is a kind of genome scale CNV ...
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How to find essential genes by differential expression from TCGA 3rd level CNV data? [closed]

I have two types of data one have normal patients copy number variation (CNV) data and another have tumor patients CNV data. In each file there are three columns one contain patient ID, second ...
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3 votes
1 answer
39 views

Database for germline copy number variations in cancer

I am interested in looking at germline copy number variations in individuals that are at high risk of developing cancer. Are there any databases where I can look, if a CNV seen in our test case has ...
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1 vote
1 answer
317 views

cn.MOPS fails with 'missing value where TRUE/FALSE needed'

I am trying to use cn.MOPS to call CNVs on a set of whole exome sequencing data bam files. My script (up to the point where it fails) is: ...
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2 votes
1 answer
142 views

Save output to a specific folder and/or with a specific prefix in Cancer Genomics Cloud

I would like to run the CNVkit workflow on Cancer Genomics Cloud. However, the two workflows that I'd like to use: CNVkit Reference, for building a reference from normal samples CNVkit CNV Calling, ...
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1 vote
1 answer
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Parallel version of cn.mops' bamDataRanges

I am trying to run cn.MOPS to detect CNVs in multiple bam files. Following the example code, I have run: ...
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4 votes
1 answer
102 views

Simulate and test CNV workflow?

I'd like to evaluate a CNV project. My aim is to evaluate if the scripts are sufficient for calling reasonable CNVs. I know they have a paper, but their scripts may be buggy... and all papers are ...
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2 votes
1 answer
64 views

Comparing two files with overlapping regions and get their associated information

I have two file that have overlapping regions. One file has chromosomes, position, CNV data and samples.Other file has chromosomes, positions and ensemble ids of genes. Here is some lines of two ...
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1 vote
0 answers
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Detect gene duplication events from a whole genome in FASTA format

Are there any tools for finding duplications from a whole genome in FASTA format? Let's say the genome has gene A duplicated somewhere in the genome and gene B triplicated in tandem elsewhere in the ...
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1 vote
0 answers
64 views

Normalize by counting CNV within a pool of VCF files

I’m (trying) using the GATK4 germline CNV calling pipeline. I successfully got 57 VCFs from my sample batch, called with segments (obtained by merging the contiguous intervals), like in a classic VCF :...
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4 votes
1 answer
93 views

Compute copy number from cases and controls

I have some data on Copy Number Variation (SNP chip) for a population of samples. In particular, I have a set of samples (considered as cases) which display a specific disease phenotype, and another ...
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1 vote
0 answers
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Methodologies for CNV analysis on SNP chip data

I'd like to analyze some Copy Number Variation data produced with SNP chip technologies. Data is provided using contingency tables, i.e. for each gene it is provided: ...
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2 votes
0 answers
83 views

how to plot LD between SNPs and CNVs

I have a bunch of CNVs which I have estimated LD between each allele of CNV with all SNPs across the entire human genome. I used my R-script to do a pairwise LD analysis. The following is the first ...
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2 votes
1 answer
145 views

how to count the number of each allele of CNVs?

I have a bunch of files (vcf format) each containing site and sample annotations of a copy number variant (following example is part of one of my files, I am showing 11 individuals but they are nearly ...
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7 votes
2 answers
460 views

VCF merge containing CNV

How do I merge VCFs files containing CNVs? I use vcf-merge, a VCFtools function, and after bgzip and tabix, SAMtools, to index and tab separate variants, but I don't know if it is the right way.
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3 votes
1 answer
298 views

Database of copy number alterations in different cancer types

Is there a database of somatic copy number alterations (CNAs) in different cancer types? That is, annotations of which CNAs are more commonly seen in different cancer types.
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5 votes
1 answer
47 views

Does GISTIC (v 2.0) estimate amplified/deleted probabilities on a single sample basis?

Does GISTIC 2.0 estimate the background model: G = -log(Probability | Background) by permuting within the sample or across all samples in the set? The paper ...
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