Table 4 Number of single nucleotide polymorphism (SNPs) recovered after various filtering stages for five species of shelled pteropods. Hard-filtering was implemented in GATK3.8 VariantFiltration using the following settings: QualByDepth <2.0, FisherStrand >60.0, RMSMappingQuality <5.0, MQRankSumTest <-5.0 and ReadPositionRankSum <-5.0. The hard-filtered SNPs were subsequently filtered to keep those with a minimum site coverage of 5x and present in at least 80% of the individuals. Other filtering options were less stringent, such as a minimum depth of 2x and site presence in at least 50% of individuals

From: Novel genomic resources for shelled pteropods: a draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance