Access To Multiple Sample High-Throughput Sequencing Diploid Data With Snps Validated With Orthogonal Technology (E.G. Sanger Sequencing, Microarray)?

Question

[mubozhi]

I have been searching for this on-and-off for many months. Basically, I am looking for FASTQ or BAM files (preference for Illumina) of multiple samples of a diploid organism, where there is also a "gold standard" or "benchmark" set of validated SNPs for each sample. The SNPs should not be validated with another high-throughput/next-generation sequencing platform, but with an orthogonal technology, like Sanger sequencing or microarray analysis. Any diploid organism is welcome. Since I would like data from at least 3 distinct samples, the sample data can be from the same pedigree and/or come from different sources/labs.

Thank you for your consideration!

Answer 1

[rbagnall]

The 1000 Genomes project used Illumina Omni genotype arrays on some of their samples, and Affymetrix Axiom genotype array on some samples.

See this excel file, showing which samples were genotyped using Omni or Axiom, and which type of sequencing was done too. This also shows the short read archive (sra) individual accession number so you can retrieve the desired fastq files

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20111108_samples_pedigree/20111108_1000genomes_samples.xls

It also has the links to the ftp folder containing the omni and Axiom genotype data in vcf file and genotype intensity CEL files.