31 snp calling soiware packages gatk the genome

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Unformatted text preview: system noise from actual varia/on. •  Work by modeling various error types and the expected distribu/on of calls under homozygous reference (AA), homozygous variant (BB) and heterozygous variant (AB) states. •  Confidence in calls is generally affected by the reported sequence quality values and read depth. •  Most SNP callers work by comparing individual samples to a reference. 30 Common Sources of Errors •  Misalignment due to pseudogenes, repeated genomic segments, or close orthologs. –  co ­alignment of reads arising from different genomic regions can result in a false posi/ve call. •  Another source of error can be local misalignment due to indels in reads. •  Work for diploid DNA, and...
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