<p>Hi folks.</p>

<p>I'm fine-mapping an association to a gene using next-generation sequencing data in African-Americans. I have a list of a few thousand variants on chromosome 12 listed by position based on UCSC hg19 build 36. </p>

<p>I want to retrieve the reference/variant alleles and minor allele frequency from 1000 genomes project for YRI samples for comparison to my own sequencing data. How might I best do this without downloading the 1000 genomes data and recomputing allele frequencies? Is there a way to query ensembl or UCSC for this information?</p>

<p>Thanks in advance.</p>

<p>Thanks for all the responses. I actually got a very helpful response from a friend of mine. It was dead simple to download and compile vcftools and tabix on my virtual linux system. It took about 30 seconds to download my genotype calls of interest from 1000 genomes using tabix:</p>

<pre><code>tabix -f -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/supporting/AFR.2of4intersection_allele_freq.20100804.genotypes.vcf.gz 12:101266000-101422000 &gt; afr.vcf
</code></pre>

<p>Then less than a second to analyze this data for allele frequency using vcftools:</p>

<pre><code>vcftools --vcf afr.vcf --freq --out freq-afr
</code></pre>

<p>Which gives me exactly what I want.</p>

<pre><code>CHROM    POS    N_ALLELES    N_CHR    {ALLELE:FREQ}
12    101266049    2    348    A:0.87069    G:0.12931
12    101266292    2    348    A:0.954023    T:0.045977
12    101266307    1    10    G:1
12    101266725    1    10    T:1
12    101266729    2    348    G:0.991379    A:0.00862069
12    101266756    2    348    T:0.985632    G:0.0143678
</code></pre>

<p>Now, I have frequency info for my data mapped to UCSC hg19/b36. Now I just need to figure out how to match these up to the 1000 genomes frequencies using their positions.</p>
