DNA sequence of genes from vcf file

Question

[bioinfo8]

Hi,

I have a vcf file a_filtered_ann10.vcf annotated for 10 genes by bcftools and consists of 5 samples (details here). I have visualized the vcf file in IGV and can see the variation with respect to the reference.

I would like to retrieve the DNA sequences of 10 genes for all 5 samples as well as their alignment with the reference, so that I can translate them to proteins and later compare with that of reference protein sequences.

I have gone through this, but not helpful.

Any guidance would be appreciated.

Thanks!

[Pierre Lindenbaum]

, so that I can translate them to proteins and later compare with that of reference protein sequences.

how about just using something like VEP or SNpEff ?

[WouterDeCoster]

so that I can translate them to proteins and later compare with that of reference protein sequences.

Would it be easier to just annotate the vcf (e.g. using snpeff or VEP) to get the changes to the protein sequences? Based on the information you gave you are overcomplicating this.

[bioinfo8]

ensembl-vep package or its web-based tool. Will it retain sample names information?

[WouterDeCoster]

It will just add a lot of information to your vcf.

[cpad0112]

you can try FastaAlternateReferenceMaker from GATK

Answer 1

[Emily]

There's a new tool in the VEP package called Haplosaurus (still just in script mode, hence not been fully shouted from the rooftops) which will give you individual gene sequences from phased VCFs: https://github.com/Ensembl/ensembl-vep#haplo

[bioinfo8]

I used VEP web-based tool which gave pie distribution for most (not all) of the genes (individual vcf files for genes were uploaded, for e.g. gene1.vcf, gene2.vcf etc. from a_filtered_ann10.vcf). Further, I can see only very few entries in the output which corresponds to the pie distribution.

[Emily]

If there is a problem with your VEP output, please email details to helpdesk [at] ensembl.org and we'll look into it

Answer 2

[Whoknows]

Hi

You could create a table consists 3 columns like below and then go to Ensemble -> Biomart section -> in Filtration section you could import this list and get fasta file based on selected regions.

Chr   Start   End
12    100000  20000

Answer 3

[songbaoxing168]

I have a software designed for this purpose.

https://github.com/baoxingsong/AnnotationLiftOver