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Hi, can someone explain what are the differences between targets and baits in exome sequencing? I'm running picard HsMetrics to compute some statistics for exome seq bam files. I've read that "bait" and "target" are very similar in other threads but I'd like to understand the concept behind the two. I'm currently using the same file for data prepared using Agilent SureSelect.
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Well the targets are the things you're trying to capture (generally exons). The baits are the things you use to do the capture.
They don't always overlap as much as you think. Sometimes a bait will be offset to a target due to thermodynamic constraints on positioning or design algorithms trying to avoid repetitive/low complexity sequence.
Hence a read can be:
On bait and on target
On bait but off target
Off bait and off target (noise)
Generally it doesn't matter if you use the targets file to define the metrics - after all, that is what you're interested in. It's not like you're going to go and assess the performance of all the baits in a SureSelect kit..
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