Questions tagged [cnv]

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

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Are there any simple ways to call copy number variants from a Nebula Genomics WGS data?

I want to find my copy number variants. I got DNA testing from the Nebula Genomics and received the raw datas in .cram, .fastq, .vcf formats. Are there any simple and easy method to call my copy ...
if0615's user avatar
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3 votes
0 answers
69 views

Issue creating CNV plot from WES data

I received Whole Exome Sequencing data from an NGS company (CARIS, specifically). I received R1 and R2 FASTQ files, a BAM file aligned to hg38, and a VCF file. I used CNVPytor to create a CNV plot (...
InterestingQuestions44's user avatar
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Adding BAF and Log2 ratio to VCF file

I have access to pre-processed VCF files from a genetic dataset, and am trying to use the MoChA tool to calculate mosaic chromosomal alterations in this dataset. However, MoChA requires BAF and ...
Akshaj Darbar's user avatar
2 votes
0 answers
15 views

consortium, biobank or browser with CNV eQTLs

I found that GTEx contains several SNPs eQTLs, but I'm looking for previously reported CNV-eQTLs, where can I find such data (freely available)?
Caterina's user avatar
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2 votes
0 answers
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datasets or biobanks with both (WGS or genotype intensity) and methylation data

My aim is to associate CNVs to DNAm, but I don't know where to find datasets which contain both (sequencing + methylation). Do you know any?
Caterina's user avatar
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1 vote
2 answers
862 views

Plotting infercnv results

I'm working with matched single cell data, where we have treated and untreated samples for the same patient. I ran CNV analysis using the infercnv package. I've ...
mmpp's user avatar
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2 votes
1 answer
91 views

CNV Kit ` from . import commands ImportError: cannot import name 'commands' from '__main__'`

I am trying to run some code for my colleague in bash ...
Indira's user avatar
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-1 votes
1 answer
67 views

GATK g CNV code Aborts Before Running Main Code

I have been struggling to get the code I wrote for running GATK g CNV on my Linux machine (Steps Here: https://gatk.broadinstitute.org/hc/en-us/articles/360035531152 ) to work. Specifically it seems ...
Indira's user avatar
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1 vote
1 answer
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what does ALT ID DUP refer to when ALT ID for copy number are already specified?

ALT ID CN2, CN3,CN4,CN5 are regions of elevated copy number relative to the reference, Then what does the ID =DUP separately cover? I am new to these analyses. please help ...
Anubrata Das's user avatar
2 votes
1 answer
120 views

CNVKit does not output all the accessible regions in the targets bed file

This question was also asked on Biostars I am using CNVkit on my data using hg38 as reference. The command that I am using is the following: ...
ashenflower's user avatar
1 vote
0 answers
38 views

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 ...
Thanh Nguyen's user avatar
2 votes
0 answers
56 views

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 ...
newbiocoder's user avatar
2 votes
0 answers
185 views

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 ...
gc5's user avatar
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4 votes
0 answers
46 views

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 ...
gc5's user avatar
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1 vote
1 answer
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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 ...
gc5's user avatar
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1 vote
1 answer
31 views

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. ...
Angelo's user avatar
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0 votes
1 answer
92 views

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....
Praveen's user avatar
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2 votes
1 answer
41 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): ...
Stephanie Hoyt's user avatar
-4 votes
1 answer
65 views

How to visualise the proportion of clonal genes to sub clonal genes [duplicate]

I have a data frame ...
Zizogolu's user avatar
  • 2,148
-1 votes
2 answers
72 views

Calculating the number of probes for a given genomic range

I have a big data frame like this for copy number (exome seq) ...
Zizogolu's user avatar
  • 2,148
2 votes
0 answers
61 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 ...
Zizogolu's user avatar
  • 2,148
0 votes
1 answer
90 views

Joining columns to a sorted file

I have had a segmentation file (copy number) like below ...
Zizogolu's user avatar
  • 2,148
1 vote
1 answer
64 views

What does this statement mean?

I have a copy number segment file with this by SCAT R package ...
Zizogolu's user avatar
  • 2,148
2 votes
2 answers
70 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 ...
unicorn's user avatar
  • 211
0 votes
1 answer
27 views

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 ...
unicorn's user avatar
  • 211
2 votes
2 answers
47 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 ...
unicorn's user avatar
  • 211
3 votes
1 answer
63 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 ...
Aprasad's user avatar
  • 31
1 vote
1 answer
471 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: ...
terdon's user avatar
  • 10.1k
2 votes
1 answer
159 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, ...
gc5's user avatar
  • 1,783
1 vote
1 answer
104 views

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: ...
terdon's user avatar
  • 10.1k
4 votes
1 answer
133 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 ...
SmallChess's user avatar
  • 2,699
2 votes
1 answer
87 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 ...
Sarah's user avatar
  • 105
1 vote
0 answers
102 views

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 ...
Biomagician's user avatar
  • 2,459
1 vote
0 answers
73 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 :...
Tintest's user avatar
  • 11
4 votes
1 answer
94 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 ...
gc5's user avatar
  • 1,783
2 votes
0 answers
56 views

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: ...
gc5's user avatar
  • 1,783
2 votes
0 answers
118 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 ...
Anna1364's user avatar
  • 516
2 votes
1 answer
154 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 ...
Anna1364's user avatar
  • 516
7 votes
2 answers
646 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.
Andrea Spinelli's user avatar
3 votes
1 answer
312 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.
719016's user avatar
  • 2,324
6 votes
1 answer
63 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 ...
Emanuel's user avatar
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