What are the differences (in terms of accuracy) in using default and custom interval list (-L) for variant calling on exome sequencing data?
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6.6 years ago
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In exome sequencing, specific interval list (-L) is used by each company to capture particular region. But all exome in the genome will be in particular regions (the default region of exomes mentioned here). So what is the difference between using custom interval list (-L option used in GATK best Practice mentioned here and default interval list. How the accuracy of the output is affected?

RNA-Seq sequencing exome sequencing • 1.8k views
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6.6 years ago
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there is a post regarding interval list here. Why cant we use default interval list

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