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9 votes

Is there an easy way to create a summary of a VCF file (v4.1) with structural variations?

According to the bcftools man page, it is able to produce statistics using the command bcftools stats. Running this myself, the ...
gringer's user avatar
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9 votes
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How to read structural variant VCF?

I just received a reply from 1000Genomes regarding this. I'll post it in its entirety below: Looking at the example you mention, I find it difficult to come up with an interpretation of the ...
Devon Ryan's user avatar
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8 votes
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Remapping genomic coordinates to account for indels

I think that you need a LiftOver Chain file to transform your coordinates. You can obtain such a file using bcftools consensus with the ...
Karel Břinda's user avatar
7 votes
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Given a VCF of a human genome, how do I assess the quality against known SNVs?

To achieve (at least some of) your goals, I would recommend the Variant Effect Predictor (VEP). It is a flexible tool that provides several types of annotations on an input .vcf file. I agree that ...
Kevin's user avatar
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6 votes
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Why are inversions defined as the reverse complement and not just the reverse of the reference?

If an inversion were just reversed then there would be 3' -> 3' bonds and 5' -> 5' bonds. That's why inversions are reverse complemented, you then maintain the normal 5'->3' direction. This is nicely ...
Devon Ryan's user avatar
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6 votes
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Is there an easy way to create a summary of a VCF file (v4.1) with structural variations?

The "my own parser" solutions. The information I was searching for in part of column INFO, namely in variables SVLEN ...
Kamil S Jaron's user avatar
6 votes
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How can I call structural variants (SVs) from pair-end short read resequencing data?

I think the best method or combination of methods will depend on aspects of the data that might vary from one dataset to another. E.g. the type, size, and frequency of structural variants, the number ...
roblanf's user avatar
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5 votes

Given a VCF of a human genome, how do I assess the quality against known SNVs?

The greatest protein coding variant catalogue is definitely ExAC (>65k individuals). They also published a blogpost where they describe how to reproduce figures in the paper (it is a good start how to ...
Kamil S Jaron's user avatar
5 votes
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Detecting structural variants with MinION data

There was a Structural Variant breakout session at the London Calling conference this year. Unfortunately I didn't attend that session, but MinION community members have access to Constance Donnell's ...
gringer's user avatar
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5 votes
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After artificially creating events in a FASTA file, how do I keep track of the old coordinates?

I've written a handful of programs from scratch to simulate mutations and variations in real or simulated sequences. The trick has always been to sort the variants by genomic coordinate, apply the ...
Daniel Standage's user avatar
4 votes

After artificially creating events in a FASTA file, how do I keep track of the old coordinates?

If you look for a program which would randomly introduce SNPs + short indels and then would save everything into a VCF file, DWGsim or Mason Variator could be a good choice. Then you can create a ...
Karel Břinda's user avatar
4 votes

How to read structural variant VCF?

So, first off, as others have pointed out, I'm pretty sure that example is just wrong. At least, the numbers don't match as you've pointed out. That said, it is impossible to be sure without showing ...
terdon's user avatar
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4 votes

Given a VCF of a human genome, how do I assess the quality against known SNVs?

Your best bet is to use programs that provide you an complete annotation of variants present in your VCF. Two examples are snpEff and Annovar. These programs work on known variants deem different ...
nuin's user avatar
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4 votes
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Quality GL entries in vcf file

The VCF spec clearly states that these are indeed log likelihood values: • GL : genotype likelihoods comprised of comma separated floating point log10-scaled likelihoods for all possible ...
terdon's user avatar
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4 votes
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BED file from .bam alignment structure

I cannot access the pipeline from nanopore, but looking at the python script you provided: ...
StupidWolf's user avatar
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4 votes

Difference between genome assembly and genome sequence alignment to a reference to find structural variants

the first being what the 1KGP and SDGP did and sequence the whole genome, align the reads to the reference genome and end up with a BAM file. If you have a well defined reference genome (e.g. human, ...
Chris_Rands's user avatar
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3 votes

Finding matched genes for each genomic range

You received an answer from Kamil for a similar question here: https://bioinformatics.stackexchange.com/a/8532/650 You can adapt the code they gave you to compare ...
Ram RS's user avatar
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3 votes
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Simplest way to work out structural variant type?

GRIDSS's author had posted his own solution on Github. The code is: ...
SmallChess's user avatar
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3 votes

Is there a standard tool used to convert a VCF to a BEDPE?

SURVIVOR has a subcommand to convert an SV vcf to bed, although I'm not sure if it's actual bedpe format. To install: ...
Wouter De Coster's user avatar
3 votes

How do I find split reads?

The answer to this question depends on the aligner used to generate SAM/BAM file. For BWA method that is part of the pipeline mentioned in comments, split reads will be flagged as supplementary ...
Mehrdad Bakhtiari's user avatar
3 votes

How can I call structural variants (SVs) from pair-end short read resequencing data?

In case if you are really dedicated to obtain perfect results, you can use strategy described there, in 1000GP 3rd Phase SV detection paper - use these tools, validate your calls with IRS test, merge ...
German Demidov's user avatar
3 votes
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What is the exact definition of "breakend"?

A structural variant is an inversion, deletion, duplication, or translocation. A "breakend" is one endpoint of a structural variant. This paper (Alkan et al. Nature Review Genetics 2011) ...
user11883's user avatar
2 votes

Is there an easy way to create a summary of a VCF file (v4.1) with structural variations?

For structural variants I think you can use SURVIVOR like SURVIVOR stats which was design specifically for such purpose (statistics on SV file).
Medhat Helmy's user avatar
2 votes

Is there an easy way to create a summary of a VCF file (v4.1) with structural variations?

You might want to try Bio-VCF. From the authors description Bio-vcf is a new generation VCF parser, filter and converter. Bio-vcf is not only very fast for genome-wide (WGS) data, it also comes ...
eastafri's user avatar
  • 319
2 votes

Remapping genomic coordinates to account for indels

If the goal is to extract the consensus sequence for given regions, this is how it works in 2019. bgzip and index your vcf file....
finswimmer's user avatar
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2 votes

Structural variant calling for low-coverage PacBio data

There is an evaluation of PB Honey and Sniffles algorithms for low coverage PacBio datasets in this preprint and another evaluation is shown on this poster. Both reports agree that optimal is (...
Kamil S Jaron's user avatar
2 votes
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RSVSim insertions from chr1 to chr2

Answer eventually found on the BioConductor post: https://support.bioconductor.org/p/114354/#114585 It basically comes down to not using RSVSim, but other R packages. Final code snippit: ...
Fini's user avatar
  • 153
2 votes
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Can I pilon-polish long reads with Illumina short reads to improve structural variant detection?

I'd recommend using Canu for correction rather than Pilon, because it has a component that is specifically designed for read-level correction. The newest version of Canu (v1.7) will track all reads ...
gringer's user avatar
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2 votes
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Generate table for total number of SV events per sample

So you have data in "long format" and want to convert it to "wide format". You can use spread() from tidyr for that: ...
Devon Ryan's user avatar
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2 votes

Analyzing proteins based on sequence similarity

I suggest you give DAVID a try. Specifically, their Functional Annotation tool. Just enter your list of protein IDs, and it will return groups of proteins where particular GO functions are ...
terdon's user avatar
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