Tag: GBS

Transposition and duplication of MADS-domain transcription factor genes in annual and perennial Arabis species modulates flowering

Annual and perennial species occur in many plant families. Annual plants and some perennials are monocarpic (flowering once in their life cycle), characterized by a massive flowering and typically produce many seeds before the whole plant senesces. By contrast, most perennials live for many years, show delayed reproduction, and are…

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Filter criteria for variants based on GBS data

Filter criteria for variants based on GBS data 0 Are there recommended filter criteria for variants based on GBS data? I currently use this filter formula that is used in bcbio for WGS based variants soft-filtering bcftools –soft-filter GATKCutoffSNP -e TYPE=”snp” && (MQRankSum < -12.5 || ReadPosRankSum < -8.0 ||…

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Beagle 5.2 Imputation Issue, understanding output

Hey everyone, I’m having some trouble with the imputation step in my GBS pipeline. I’m following the FastGBS pipeline basically as written up until this point. Before running Beagle, i’ve performed a filtering step using vcftools (though I get the same error whether or not I do this; I just…

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