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Our multi-sample joint calling strategy across all cases and controls as a set enabled us to distinguish between homozygous reference and missing genotypes (Kumar et al., 2014), and provides the basis for standardized QC across aggregated data, essential for case control designs (Winkler et al., 2014).
Analysis of related samples requires joint calling within each family to provide fully informative results.
We used a multi-sample joint calling strategy across all SUDEP cases, epilepsy and disease control samples to mitigate problems caused by the heterogeneity of sequence capture kits.
Alternatively, CNVtools, performing a joint calling and association testing, might also be considered, though it is more difficult to apply than that based on LRR and takes longer to run.
This strategy was enabled by our joint calling strategy across all cases and controls, and ensured that only variants sequenced in the majority of each of the testing groups were used to calculate the per-individual burden scores.
Furthermore the success of joint calling provides a baseline to estimate the sensitivity of CNV detection when trio data are not available, such as for the case control dataset in this study.
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"He told me about this joint called Pseudo".
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There was a halal joint called Turkish Cuisine down the block, but Kanter was hesitant.
Aside: North of San Francisco, there is a coffee joint called Shaky Grounds.
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