Benchmarking

On the theory and practice of benchmarking variant callers

Comparing calls

precisionFDA strategy for standardizing comparison of variant caller results

TCGA/GDC - building a variant caller pipeline to run across the 1k genomes project

Pipeline overviews
Applies MuSe, MuTect2, VarScan2, SomaticSniper
"There is currently no scientific consensus on the best variant calling pipeline so the investigator is responsible for choosing the pipeline(s) most appropriate for the data. "

2015 Tool Normalize VCF format for equivalent representation in comparisons

2016 Infrastructure hybrid cloud/local infrastructure to process 5300 WGS

Study 2014 Database of Genomic Variants

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