SNP filtering for haploid genomes
Posted in Ask the GATK team | Last updated on 2012-10-01 17:06:04

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Does the GATK team have any recommendations for filtering SNP data for haploid genomes? Our team works with microbial eukaryotes, both haploid and diploid and we have used the GATK v3 best practices for filtering for the latter. [VQSR was not possible, since we do not have access to a truth/high confidence SNP set.]

Thanks, Mika

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