Hi all - I'm doing some work with rat (rn5) and am using GATK to recalibration quality scores. GATK's VariantRecalibrator requires a set of high quality SNPs (in VCF format) in order to train its model. The resource I have is a list of all variants (dbSNP) I obtained from Ensembl. Is there a subset of SNPs that are considered high-quality? Or better yet, has anyone else collated a dataset of high-quality SNPs for use with GATK?
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NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM
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