Doubt on filtering data from .VCF file

Question

[brunobsouzaa]

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 mispelling!

[iraun]

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 straight 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 software 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.

[Pierre Lindenbaum]

Want to know something terrifying? There are people currently analysing whole exome variant data using Excel. I kid you not.

— Daniel MacArthur (@dgmacarthur) October 25, 2012

[brunobsouzaa]

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.

Answer 1

[Dhana]

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

Use the package VariantAnnotation and GenomicFeatures from Bioconductor. It will be useful for your analysis.

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