I am doing a project that requires bench-marking the performance of computational tools for alignment and variant calling of human genome sequencing data. In particular I would like to establish benchmarks comparing the performance of GATK and ADAM/Avocado.
My main question is which genomic data-sets should I use as the input to the data processing pipeline. In Frank Nothaft's (author of ADAM and Avodaco) thesis he reports bench-marking the processing of NA12878 from the 1,000 genome's project in Avocado as compared to GATK's HalotypeCaller. He also reports benchmarking on 270 samples from the Simons Genome Diversity Data-set.
I am interested in reproducing this portion of his work, but do not know where I can get a hold of these datasets. Where can I get a copy of the NA12878 genome (BAM file) and also were can I get aligned samples from Simons Genome Diversity Data-set?