Question: Viltering VCF file with Exonic variants via Python
0
gravatar for a_biologist
4.1 years ago by
United States
a_biologist0 wrote:

Hello All,

I have a VCF file and I want to filter the file with exonic varients only and through out the intronic ones. I have done it using a python script but it still not doing it so and the run takes a long time to do so. Is there a faster way to do this?

 

 

Thanks.

next-gen • 1.5k views
ADD COMMENTlink modified 4.1 years ago by Pierre Lindenbaum119k • written 4.1 years ago by a_biologist0
2

So you are just trying to identify exonic variants? Try using Annovar or KGGSeq

ADD REPLYlink written 4.1 years ago by Sam2.3k

Hi Sam, I could do that but instead I want to filter out only variants that are with an exonic region I don't want them annotated for the time being just get a new resulted vcf file that is filtered with exonic variants and that's why I used python to do so.

Thanks

ADD REPLYlink written 4.1 years ago by a_biologist0
1

Well, once you have them annotated, you can just get the coordinates of those snps that you want and use any programme you like to filter them from the vcf file. It will be much faster and simpler, no point in reinventing the wheel unless you are trying to develop a new programme

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by Sam2.3k
2
gravatar for Devon Ryan
4.1 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

Just use bedtools intersect and provide it with your VCF file and a BED file containing the exons (I'm not entirely sure this would work with a GFF file, since it might then give you anything overlapping a gene).

ADD COMMENTlink written 4.1 years ago by Devon Ryan89k
2
gravatar for fashiondesignrussian
4.1 years ago by
Belarus
fashiondesignrussian50 wrote:

Try VCFMiner from Mayo, latest releases of DNAstar software suite have also some tools to play with VCFs, try R packages, perhaps

ADD COMMENTlink written 4.1 years ago by fashiondesignrussian50
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