How to get SNP annotations (hg19/38) for GWAS data

Hello,

I am looking to get the SNP annotation file which looks something like this

snpid chr pos
Snp_01 1 721289
Snp_02 1 752565

It should have an SNP id, chromosome location, and position. How can I get this information

snp

• 958 views • link

written 5.6 years ago by AHW •

What have you tried? Have you looked at NCBI eutils?

• 0 views • link

written 5.6 years ago by Ram

0 answers

No answers yet.

More posts like this

Intersecting phyloP bed and per-base bed files
written 5.0 years ago by gokberk

Hi, I'd like to intersect the phyloP bed file with a SNP-based bed file using bedtools. By "SNP-based" I simply mean a list of SNPs …
VCF file ID missing
written 6.2 years ago by tothepoint

I am working with WGS data and ran GATK pipeline. We are currently studying selective sweep gene study and I encountered this issue of missing …
TCGA SNP analysis using manhattan plot and QQ plot
written 8.2 years ago by DanielC

Dear Friends, I am new to TCGA data analysis. I would really appreciate your suggestions on these questions: a) From TCGA vcf files, I am …
Mapping a chromosome position with Gene ID
written 9.4 years ago by Paul

I am trying to map chromosome positions with all the gene IDs available. The position file1 I have looks like this #CHROM POSID REF ALT …
NCBI Gene(Nucleotide sequence) to chromosome location
written 9.6 years ago by stanedav •

Hello, recently I am working on my own pipeline in python. I am downloading page from NCBI Sequence viewer with defined ID (NM_000304.3) in this …
Get a table of minor an major allele from a vcf file
written 9.9 years ago by shinken123

Hi Probably this question have a simple answer but I could not find it until now. I have a VCF file that integrates the data …
Querying hg19 reference genome
written 11.1 years ago by mdhale121 •

Hello, Is there an easy way to query the hg19 reference genome based upon position and chromosome combination? I do not want to download the …
merging coverage and gene annotation
written 11.3 years ago by schelarina •

Hello, I have an RNAseq coverage per position file created with bedtools. I would like to include in this file an additional column containing the …
retrieve with tabix only fields of interest
written 11.4 years ago by tonja.r

I am using tabix to retrieve information in a specific genomic region. need not the hole information but only let say second and the third …
Assigning locus to set of SNPs based on its chromosome position
written 11.7 years ago by iphoenix2100 •

Hi all, So I have this tab-delim file with information on (following columns) SNP CHR POS Allele1 Allele2 A.Freq1 Effect StdErr P.value Now I would …