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Forum: Benchmark toolkits for Diploid Variant Calling

This is a post to compile all the current toolkits to evaluate/benchmark Diploid Variant Calling. Feel free to contribute as comment or editing the post.

Smash - https://github.com/amplab/smash

variant-calling benchmarking
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updated by Ram Ram • written by 14134125465346445 14134125465346445

Not a toolkit, but Brad Chapman's blog contains about enough relevant comparisons that it should probably get a mention anyway.

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written by Devon Ryan Devon Ryan

1 answer

My hapdip benchmark. It consists of two complement components: a benchmark on a pair of haploid-diploid samples (see this) and a benchmark on GIAB's high-confident regions. The former gives an unbiased global view of error rates. The latter measures how we can reduce errors in well-behaved genomic regions.

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updated by Ram Ram • written by lh3 lh3

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