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Benchmarking for comparing diffent variant callers

Hey,

I have to do some variant calling in a plant organism (diploid)

I have selected the programs I want to test before I use my own data. (Freebayes, Samtools, SOAPsnp and Cortex_VAR.) However i am struggling to come up with a reference to compare the tools against. First i want to test the software before i can use it on my own data.

Is there a benchmark i can use or is it better to simulate my own reference? and use the tools accordantly

Regards, Covux

snp benchmark variant calling
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updated by igor igor • written by Covux • Covux

2 answers

use 'Genome in a Bottle' data ? http://jimb.stanford.edu/giab/

e.g: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/

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written by Pierre Lindenbaum Pierre Lindenbaum

There are a few public reference genomes listed here: http://googlegenomics.readthedocs.io/en/latest/use_cases/discover_public_data/genomic_data_toc.html

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written by igor igor

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