Questions tagged [structural-variation]

Refers to large-scale genomic variation in a population or between individuals, including inversions, translocations, and copy number variants

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Pindel has an extremely large output

I am wondering if I am doing something wrong here. I ran Pindel (alongside two other SV callers) on four WGS samples. The two other callers report approximately 50000 SVs and have a decent running ...
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Analyzing proteins based on sequence similarity

Using NCBI Gene database, I retrieved list of 7015 protein which are implicated in autism pathogenesis. This list includes tax-ID, organism name, symbol, aliases, map location, chromosome, genomic ...
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BED file from .bam alignment structure

I am using a pipeline from nanopore to detect structural variants (SVs) in a human sample with long-reads sequencing. The first steps of the pipeline are: index the reference genome with ...
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Is there a standard tool used to convert a VCF to a BEDPE?

Many popular SV callers output a VCF. Unfortunately, there isn't a unified system at the present to label events with the same notation. However, is there a standard method for converting these VCFs ...
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Quality GL entries in vcf file

I have a vcf v4.2 file with structural variants, the 8 columns describing the variant are clear, but in the genotype information I got confused by values of ...
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Finding matched genes for each genomic range

I have called structural variants and now I have ...
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Generate table for total number of SV events per sample

I have called and annotated structural variants and I have a table by name of samples and structural events like below ...
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59 views

Delly finds identical deletions with different consensus sequences

I am using delly to call structural variants on a human WGS sample. I noticed that it finds certain variants that are essentially duplicates. For example: ...
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798 views

How do I find split reads?

How can I detect a split read in a BAM file? Is there any sign in the CIGAR string that describes split read?
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Is there a risk in inference of structural variations using mate-pairs?

Inference of structural variants from short read data is always sneaky (for a question about pair-end reads, see this). Recently I bumped into a paper where they used mate-pairs for inference of ...
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structural variants: why doesn't AS + AP = SU?

I have run smoove then duphold on 46 individuals, then pasted the duphold output back into a squared vcf with all 46 samples. I have been using SU/AC as one of my filters, looking for variants that ...
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Visual representation of detecting deletion by different read types

I'm having some trouble differentiating between CNV, split reads and read pairs and how each one elucidates the presence of a structural variation, say deletion. Given a reference and donor sequence,...
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RSVSim insertions from chr1 to chr2

edit explaining python tag I would still rather have a solution based on the RSVSim package in R, but while waiting for someone who might have an answer I wanted to look at other solutions as well. ...
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Simplest way to work out structural variant type?

In VCF 4.2, a structural variant (SV) can be described with the BND keyword in SVTYPE. For example, the following example is an ...
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Complete Genomics Junction file for SV Detection

At present, I have vcf file for each patient generated from tumor data. I am using virtual normal correction method for somatic mutation detection because I don't have normal data. For SNP or small ...
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549 views

Can I pilon-polish long reads with Illumina short reads to improve structural variant detection?

I have pacbio Sequel data at 50 x coverage for a strain of animal. I would like to find structural variants compared to the reference genome sequence. At the moment, I align my reads to the reference ...
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How to install and use pbhoney on Mac OSX?

I download the PBSuite from SourceForge. I decompressed the file. I then moved to this directory: PBSuite_15.8.24/pbsuite/honey and typed: ...
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Can Mauve export indels or is there an whole-genome aligner that can export indels?

I have aligned two whole genomes of the same species in Mauve using progressiveMauve. One of the genomes is 2 megabases longer than the other so I know it must contain some insertions. Looking at the ...
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Can structural - equation modeling be used in Bioinformatics?

I am a bioinformatics student and I was learning the basics of structural equation modeling (SEM). I was wondering, are there any applications of SEM on bioinformatics? Are there any strong sides ...
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Why are inversions defined as the reverse complement and not just the reverse of the reference?

I can’t quite understand the way inversions are defined. In particular I expect an inversion to be only a reversed version of the reference and not its reverse complement. Most sources use diagrams ...
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After artificially creating events in a FASTA file, how do I keep track of the old coordinates?

I'm beginning with the reference genome in FASTA format, hg19. I am reading the sequence into a Python dictionary with BioPython: ...
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182 views

Detecting structural variants with MinION data

Working on various cancers I have an interest in detecting structural variation (SV) in human, we've successfully used various tools like Pindel, SVDetect, Manta, and LUMPY, to name a few for ...
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Structural variant calling for low-coverage PacBio data

PacBio is selling ~10x PacBio SEQUEL long reads as an upgrade to Illumina data for SV discovery. In a clinical setting, the main requirements are proper sensitivity and specificity but also the ...
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Remapping genomic coordinates to account for indels

I'm interested in obtaining coding sequences of my favourite gene in all individuals from the 1000Genomes (and similar projects). I use GATK to get the right subset of variants, vcf-consensus to map ...
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993 views

How to read structural variant VCF?

The IGSR has a sample for encoding structural variants in the VCF 4.0 format. An example from the site (the first record): ...
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Is there an easy way to create a summary of a VCF file (v4.1) with structural variations?

I got a bunch of vcf files (v4.1) with structural variations of bunch of non-model organisms (i.e. there are no known variants). I found there are quite a some tools to manipulate vcf files like ...
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Given a VCF of a human genome, how do I assess the quality against known SNVs?

I'm looking for tools to check the quality of a VCF I have of a human genome. I would like to check the VCF against publicly known variants across other human genomes, e.g. how many SNPs are already ...
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How can I call structural variants (SVs) from pair-end short read resequencing data?

I have a reference genome and now I would like to call structural variants from Illumina pair-end whole genome resequencing data (insert size 700bp). There are many tools for SV calls (I made an ...