Question: Doubt on filtering data from .VCF file
0
gravatar for brunobsouzaa
5.6 years ago by
brunobsouzaa490
Brazil
brunobsouzaa490 wrote:

Hi guys,

I'm new on exome sequencing and bioinformatics analysis so I was wondering if someone could help me. I've generated a .VCF file from my exome data and now I need to see which variant is related to my disease (ocular disease). Are there any package that can perform such analysis? I'm using microsoft excel to make some initial filtering like phred score and segregation but don't know where to go from now on!!!!

Thanks and sorry for any mispeling!

sequencing • 1.7k views
ADD COMMENTlink modified 5.6 years ago • written 5.6 years ago by brunobsouzaa490
1

Excel...? If you want to do bioinformatics analysis you should seriously consider to avoid using excel, and if you are using windows, you should consider even more to change to linux os. On the other hand, there isn't a straigth way to know "OK, this variant is the one responsible of my observed phenotype". It's not as simple. First, it is important to discard as much as false positives without loosing too many true positive calls. For this, you can filter the vcf according to some parameters like, quality, coverage ...etc. You can do it using different softwares like, snpsift, vcftools... etc. You maybe want to annotate the variants (using SnpEff, or another tool), to see the effects of those variants in the genes. Furthermore, if you have a list of genes related with the studied disease, you could extract the variants falling within those genes.

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by iraun3.8k

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by Pierre Lindenbaum133k
1
gravatar for Dhana
5.6 years ago by
Dhana80
Helsinki, Finland
Dhana80 wrote:

You can try out R language, it is relatively simple to learn and efficient.

Use the package VaraintAnnotation and GenomicFeatures from Bioconductor. It will be useful for your analsysis. 

The documentation and reference can be found in ;

http://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html

http://www.bioconductor.org/packages/release/bioc/html/GenomicFeatures.html

ADD COMMENTlink written 5.6 years ago by Dhana80
0
gravatar for brunobsouzaa
5.6 years ago by
brunobsouzaa490
Brazil
brunobsouzaa490 wrote:

Thanks everyone.

Airan, I am using Linux os (Ubuntu) to perform the whole pipeline till I get the .VCF file! Thanks for your answer, I've found those tools on galaxy website, I'll try to use them. Also, I'll try to use R like Dhana said.

ADD COMMENTlink written 5.6 years ago by brunobsouzaa490
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