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
1 answer
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://gsapubftp-anonymous@ftp.broadinstitute.org/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.
Log in to answer this question.
-
How to annotate the snps we get after GWAS?
written by biotechnology415 •
-
Advanced use of snpEff
written by zion22
-
vcf file processing
written by neeraj4biotech •
-
Meaning of "EX_TARGET" in VCF files 1000 genomes
written by GabrielMontenegro
-
Problem including additional annotations to vcf using snpEff
written by sumudu_rangika •
-
Determine whether a gene is totally missing
written by Canh •
-
How to annotate SNPs, identified against scaffolds (draft genome)
written by inayat45shaikh •
-
Freebayes and snpeff give different number of SNPs
written by merodev
-
VCF file lacks alternative allele listing for most rs ids
written by devenvyas
-
How Does Dbsnp Decide If A Snp Is "Associated" With A Gene?
written by Snpdude •
