Create a UCSC chain file from a VCF

Question

[rubic]

Hi,

I have a VCF file (which contains indels as well as SNPs) obtained from an individual's DNA (from a whole genome microarray) with respect to the reference genome. Is there any tool out there the will produce a UCSC chain file wrt to the reference genome given the VCF file?

[Pierre Lindenbaum]

hu ? a chain file map the regions between two assemblies. How would you use a VCF file to build this chain file ?

[rubic]

The indels in the VCF file are in essence how the 'assembled' genome of the individual differs from the reference assembly, in coordinates. So given these indels, and hence a chain file, a personal genome can be created.

[Istvan Albert]

A VCF file is a list of local differences, many of which may be inexact, especially longer variations. It is very unlikely that they would contain information at sufficient accuracy to create an entire assembly. These files are not designed to correct for cumulative errors, yet when you remap intervals a single error can affect all subsequent coordinates.

[rubic]

That may be true or not depending on what data the VCF was generated from.

I'm just asking whether anyone knows of a script/tool out there that takes a VCF (produced for a single individual sample) and creates a chain file based on the indels in the VCF (the homozygous indels if we are to be acurate), to save me writing that myself. That's all.

[Istvan Albert]

There are two different questions here really.

1. Is, theoretically speaking, the VCF format sufficiently well specified to unabmigously describe all the differences between genomes
2. Do current tools fill in the VCF format at sufficient detail to allow a full genome reconstruction of acceptable accuracy

I don't actually know the answer to either of these. But my guess would be a no.

But I'd be happy to learn more on what actually happens in practice.

Answer 1

[rubic]

there's a very simple answer to my question and it's called AlleleSeq package.

Answer 2

[Malcolm.Cook]

I'm late to the QA party, but I hope a useful update for the contemporary searcher is the following list of options:

• vcf-consensus (part of VCFtools)- "Apply VCF variants to a fasta file to create consensus sequence."

• FastaAlternateReferenceMaker (part of Genome Analysis Toolkit - GATK) "Given a variant callset, this tool replaces the reference bases at variation sites with the bases supplied in the corresponding callset records. Additionally, it allows for one or more "snpmask" VCFs to set overlapping bases to 'N'."

• vcf2chain - (part of g2gtools) "create a Chain file from a VCF file"

• vcf2diploid (part of AlleleSeq) as suggested above by @rubic