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Parallel SNP calling with freebayes
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Freebayes is a good variant caller and an alternative to the more popular GATK. I have successsfuly used freebayes to call SNPs and INDELs on fungal genomes with good results. However, one of the main drawbacks of freebayes is that it takes a huge amount of time to call variants. This is because freebayes does not take advantage of parallel processing, as a single core is used, and there is no parameter for multithreading.