SMaSH statistics

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Associated diseases

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SMaSH specifications

Information


Unique identifier OMICS_06830
Name SMaSH
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for SMaSH

SMaSH in publications

 (2)
PMCID: 4493402
PMID: 26217378
DOI: 10.3389/fgene.2015.00235

[…] well. the bcbio.variation tool can regularize vcf files, compare them to a benchmark call set, and generate a variety of metrics, including sensitivity, specificity, and genotyping error rate. the smash benchmarking toolkit () can generate metrics for precision and recall of mappers and variant callers. a novel aspect of smash is the calculation of uncertainty of precision and recall due […]

PMCID: 4179624
PMID: 25288881
DOI: 10.4137/CIN.S13779

[…] discordance among the called variants. to facilitate the method evaluation process, talwalkar et al. proposed a benchmarking methodology for the evaluation of the human genome variant callers. their smash toolkit consists of three components: (1) short reads from ngs experiments; (2) reference genome; and (3) the validation data in standard vcf format are used to measure the algorithm […]


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SMaSH institution(s)
Department of Electrical Engineering and Computer Science, UC Berkeley, Berkeley, CA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Statistics, UC Berkeley, Berkeley, CA, USA

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