VCF file from mouse data

[jfcalderon]

Hi everyone,

I am very new to the field of NGS and bioinformatics. I have obtained the VCF file for the mouse strains that Sanger Institute has sequenced. What i want to do now is to annotate the variants from a specific chromosome and make a significant list or hopefully be able to put them in some sort of graphical display to be able to analyze these variants. I have been playing around with VCFTOOLS but it only permits VCF4 or VCF4.1 files (as opposed to the 3.3 i have). I think i can use commands to already isolate the chromosome i need to work on, but still lost on how to actually "read" this VCF and get the info out of it.

Thanks a lot for your help,

Juan

[PeteH]

Hi Juan,

I have been playing around with VCFTOOLS but it only permits VCF4 or VCF4.1 files (as opposed to the 3.3 i have).

vcf-convert, which is part of VCFtools, will allow you to convert your VCF from v3.3 to v4 or v4.1. See http://vcftools.sourceforge.net/perl...ml#vcf-convert for the documentation.

I think i can use commands to already isolate the chromosome i need to work on, but still lost on how to actually "read" this VCF and get the info out of it.

By "read" do you mean what do each of the VCF fields mean? If so then I suggest you read the VCF specification. There is lots of useful information in these documents (though it may be more than you're looking for, particularly if you are new to bioinformatics); they are available here http://vcftools.sourceforge.net/specs.html. If by "read" you mean software that use VCFs as input then there are several options such as VCFtools, the Genome Analysis Tool Kit (GATK) and the Integrative Genomics Viewer (IGV) - it all depends on what you are wanting to do with the VCF.

I'm happy to help you with any specific questions you might have.

Cheers,
Pete

[jfcalderon]

Thanks a lot Pete,

1. I will try VCF convert. i assume that i only need the FASTA reference file for the chromosome i extracted my VCF for.

2. I need to extract the variants to be able to interpret them. Are they in a CDS, promoter, etc....

Thanks again,

Juan