Help With Retrieving Snps And Indels From Fvb Mouse (Vcf File)

Question

[Johnathan]

Hi everyone!

I am looking at co-occurring events in transgenic FVB mice tumours. First, I need to filter out snps and indels. I was reading the following paper: Sequencing and characterization of the FVB/NJ mouse genome by Wong et al. 2012. The research group has identified snps and indels in the FVB with next-gen sequencing. I am trying to retrieve this data that is stored in a huge vcf file at the Wellcome Trust Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/)

The file is huge and contains the genetic information of 18 different mouse strains (including FVB). I downloaded tabix/cvftools and installed their binaries to my PATH. My problem is that I don't know how to extract the SNP/indel coordinates (and what they are) from this file. I have already spent quite some time reading the documentation and googling, but I am stuck.

Has anyone done something similar? I would greatly appreciate if someone could please give me some hints.

Thank you!

Answer 1

[pd3]

The VCF file is a plain text file compressed with bgzip and can be uncompressed with standard unix gzip. The coordinates are in respect to the reference genome as described in the README ftp://ftp-mouse.sanger.ac.uk/REL-1303-SNPs_Indels-GRCm38/README

There are many ways how to extract the information you need, including generic tools like awk or specialized tools listed by Ashutosh.

Yet another tool is bcftools ( http://samtools.github.io/bcftools/)

bcftools view -s FVBJN file.vcf.gz

Answer 2

[Ashutosh Pandey]

You can use the following tools :

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_SelectVariants.html

java -Xmx4g -jar GenomeAnalysisTK.jar -T SelectVariants -V [ multiple_vcf_file] --sample_name [Sample_name (FVBJN in your case) ]

Or you can try vcftools (http://vcftools.sourceforge.net/index.html)

vcf-subset -c Sample_name (FVBNJ) | bgzip -c > Sample_name.vcf.gz

Answer 3

[Alex Reynolds]

BEDOPS includes vcf2bed, with options to filter on SNVs, insertions and deletions.