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URL: https://gatk.broadinstitute.org/hc/en-us/articles/360042913231-HaplotypeCaller
Proper Citation: GATK HaplotypeCaller (RRID:SCR_028440)
Description: Software tool for identifying single nucleotide polymorphisms (SNPs) and insertion/deletion (indels) variants, offering high accuracy via local de-novo assembly of reads. It works by identifying "active regions" with potential variation, reassembling those reads, and calculating genotype likelihoods, making it superior for complex variant detection.
Resource Type: software application, software resource
Defining Citation: DOI:10.1101/201178
Keywords: identifying single nucleotide polymorphisms, insertion, deletion, indels, variants, local de-novo assembly of reads,
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