dbSNP: minor alleles for a list of SNPs

Question

[dora]

I'm looking for minor alleles generated from current 1000 genome project given a list of SNPs. For example, rs16532, its MAF is 0.3898 with C as the minor allele from 1000 genomes. Does anyone know how I can get the minor alleles from 1k genome or dbSNP for a list of SNPs simultaneously? Or where I could download this source?

Thanks!

[dora]

The output would look like:

SNP       MinorAllele   Source
rs16532      C         1000Genomes
rs165323    T         1000Genomes
rs3092950  T         1000Genomes
...

Answer 1

[Kamil]

Try using myvariant.info. You might want to use the Bioconductor package called myvariant.

https://myvariant.info/v1/query?q=rs16532&fields=dbsnp

{
    "hits": [
        {
            "_id": "chr17:g.37349710C>T",
            "_score": 16.939035,
            "dbsnp": {
                "allele_origin": "unspecified",
                "alleles": [
                    {
                        "allele": "C",
                        "freq": 0.3898
                    },
                    {
                        "allele": "G",
                        "freq": 0.6102
                    },
                    {
                        "allele": "T"
                    }
                ],
                "alt": "T",
                "chrom": "17",
                "class": "SNV",
                "dbsnp_build": 54,
                "flags": [
                    "ASP",
                    "G5",
                    "GNO",
                    "INT",
                    "KGPhase1",
                    "KGPhase3",
                    "SLO"
                ],
                "gmaf": 0.6102,
                "hg19": {
                    "end": 37349711,
                    "start": 37349710
                },
                "ref": "C",
                "rsid": "rs16532",
                "validated": true,
                "var_subtype": "unknown",
                "vartype": "snp"
            }
        },
        {
            "_id": "chr17:g.37349710C>G",
            "_score": 16.938734,
            "dbsnp": {
                "allele_origin": "unspecified",
                "alleles": [
                    {
                        "allele": "C",
                        "freq": 0.3898
                    },
                    {
                        "allele": "G",
                        "freq": 0.6102
                    },
                    {
                        "allele": "T"
                    }
                ],
                "alt": "G",
                "chrom": "17",
                "class": "SNV",
                "dbsnp_build": 54,
                "flags": [
                    "ASP",
                    "G5",
                    "GNO",
                    "INT",
                    "KGPhase1",
                    "KGPhase3",
                    "SLO"
                ],
                "gmaf": 0.6102,
                "hg19": {
                    "end": 37349711,
                    "start": 37349710
                },
                "ref": "C",
                "rsid": "rs16532",
                "validated": true,
                "var_subtype": "unknown",
                "vartype": "snp"
            }
        }
    ],
    "max_score": 16.939035,
    "took": 5,
    "total": 2
}

Answer 2

[trausch]

ANNOVAR offers a tab-delimted text file for the 1000 Genomes variants that includes the variant allele frequency (column 5, vaf) so you can directly infer the minor allele.

egrep -w "rs16532|rs165323|rs3092950" hg19_ALL.sites.2012_04.txt
5    150871912    C    T    0.13    rs165323
17    37349710    C    G    0.57    rs16532
X    135727289    A    T    0.01    rs3092950

Latest 1000 Genomes variant file from ANNOVAR should be this:

wget http://www.openbioinformatics.org/annovar/download/hg19_1000g2015aug.zip