Get Vcf File For Heparanase Gene (Hpse)

Question

[Sagi]

Hi everyone, I have some SNPs which I'm investigating on the HPSE human gene (Heparanase). I wanted to use the SNPeff program, but it seems that it gives best outputs when using the VCF format as input.

I can't seem to find the vcf files anywhere on dbSNP when looking on my wanted SNPs. For example rs11099592. Where can I get these vcf files?

On same notice, what other tools are suggested for further analysis of the affect these SNPs have on functionality of the gene? (Some SNPs are intronic)

Thanks

Answer 1

[Rok]

For VCF files I like to use Broad Institute resource bundles, you have all the data in same place and according to reference genome you prefer.

ftp://[e-mail]/bundle/1.2/

After you download the version of dbSNP you like, you should find the location of HPSE inside the genome you have chosen. And you can extract that region from VCF file using samtools.

bcftools view -S dbSNP_133.hg19.vcf 4:84213614-84256034

After this you should get all the snps included in dbSNP v133 in this specific location range.

[Sagi]

cool, I'll try that! thanks