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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How to use hgvs to project a variant list on a given protein sequence string?

I have the following protein structural variance list: ...
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How to manually curate a genome assembly for sequence variation or error?

I have a PacBio HiFi assembly of 1.1 Gb from a heterozygous species. I have aligned this assembly against a reference genome which is around 0.9 Gb. I can see that there are quite a few INDELs, ...
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Counting hexamers in fasta sequence and identify its structure (and interruptions)

I have a lot of fasta files, each one with thousand of reads containing the hexameric motif "CCCTCT". The hexameric motif is highly continuous in most cases but interruptions may occur. I ...
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Solutions to reference bias issue

I've recently learned about the reference bias issue - inability to properly map NGS reads in certain genomic regions caused by the fact that our standard genomic references are linear and do not ...
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What is the exact definition of "breakend"?

I'm reading the Manta User Guide → it is a method to discover structural variants and indels from next generation sequencing data. The word 'breakend' is used in several contexts I have searched for a ...
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Difference between genome assembly and genome sequence alignment to a reference to find structural variants

I'm trying to determine what the difference and benefits of genome assembly and genome sequence alignments are when trying to identify structural variants or transposons in populations. I've been ...
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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 structural variant [SV] callers) on four WGS samples. The two other callers ...
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2 votes
1 answer
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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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2 votes
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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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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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2 votes
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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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2 votes
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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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2 votes
1 answer
638 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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1 vote
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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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1 vote
2 answers
164 views

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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3 votes
1 answer
360 views

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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4 votes
2 answers
244 views

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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5 votes
1 answer
207 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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6 votes
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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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13 votes
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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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13 votes
2 answers
2k 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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16 votes
5 answers
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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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13 votes
3 answers
349 views

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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16 votes
2 answers
411 views

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 ...
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