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Saturday, June 29, 2013

VCF file annotation and manipulation tools

VCF (variant calling format) file, as specified in 1000 Genome
is a common file to handle the variant information from the NGS sequencing data.

many tools have been developed to manipulate, extract information with this format.
some popular ones are:
tabix for fast indexing and extracting certain regions of the whole genome.
VCFtools for many more manipulations including annotating, merging, concatenating, comparing etc.
bedtools for genomic region overlapping calculation. etc
I have some experience with the above three tools.

by the way, I have not used the GATK tools the broad Institute yet, I am sure I will have a try sometime later.

after google, I found several more:

Taser is the one I just came across
It is based on R and can extract variant info by gene names fairly easily

Again, there are so many tools out there. Depending on your needs, choose the right one for you.

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