Question: How to use wheat chromosome 3D as input for snpEff?How I can add the wheat reference genome database (I need to install 3D chromosome based database for the annotation of VCF file from 3D chromosome)?
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gravatar for pltbiotech_tkarthi
5 months ago by
CIMMYT, Mexico
pltbiotech_tkarthi170 wrote:

How I can add the wheat reference genome database (I need to install 3D chromosome based database for the annotation of VCF file from 3D chromosome.

Since I referred the manual of snpEff at: http://snpeff.sourceforge.net/SnpEff_manual.html#run

and most of the examples given here based on human genome data.

So I couldn't even find a suitable wheat genome database (with 3D chromosome homeolog) at:

https://sourceforge.net/p/snpeff/activity/?page=0&limit=100#581f1f2134309d5a077e50d9 ftp://ftp.ensembl.org/pub/

Kindly let me know concerning my request to implement the wheat 3D Homeolog databased at snpEff.

I used the model files with following script is working well:

time java -Xmx4g -jar snpEff.jar -v GRCh37.75 examples/test.chr22.vcf > test.chr22.ann.vcf
snp • 327 views
ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 5 months ago by pltbiotech_tkarthi170

Your question is unclear. With 3D genome, do you mean genome annotation derived from chromosomal conformation capture (like HiC) experiments? Do you want to match variants with something like borders of topologically-associating domains or chromosomal loops? Please clarify.

Edit: Ok, 3D is just a chromosome name. Please be more specific in the future, that will help you to get elaborate answers ;-)

ADD REPLYlink modified 5 months ago • written 5 months ago by ATpoint19k

I need to annotate the variants of my gene of interest with VCF file, physically this gene is is located at between 363599046 363598038bp in 3DL chromosome. I already did with VEP ENSEMBL server, but would like to do with snpEff as well to compare the results.

ADD REPLYlink written 5 months ago by pltbiotech_tkarthi170

what exactly are you looking for? do you want to add the wheat genome chromosome 3D to some database and you're looking for that wheat genome chromosome 3D sequence?

perhaps you can find it here ?

ADD REPLYlink modified 5 months ago • written 5 months ago by lieven.sterck5.5k

Yes, I can retrieve the chromosomal contigs from URGI-IWGSC, but I don't know how to give the chromosomal contig as an input file to snpEff.

ADD REPLYlink written 5 months ago by pltbiotech_tkarthi170
1

aha, now we're getting somewhere.

perhaps you might rephrase your question a little to be more on topic? eg something like: "how to use wheat chromosome 3D as input for snpEff" .

ADD REPLYlink written 5 months ago by lieven.sterck5.5k

Thanks Lieven Sterck, I added the rephrased question as you have written here.

ADD REPLYlink modified 5 months ago • written 5 months ago by pltbiotech_tkarthi170
1

Here is the general idea: Building Snpeff Database

Process is described in snpEff manual: http://snpeff.sourceforge.net/SnpEff_manual.html#databases

You will need to find one section under build database that you can use with the sequence and the annotation files you will get.

ADD REPLYlink modified 5 months ago • written 5 months ago by genomax69k
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