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Old 08-18-2017, 05:54 AM   #1
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Location: Kyiv, Ukraine

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Default Exome sequencing: should we do local realignment

Dear colleagues,

With ever-increasing quality of NGS platforms, is it still desirable to do local realignment for HiSeq 2500 human exome reads from an Agilent Sureselect library?

Thank you
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Old 08-18-2017, 05:08 PM   #2
Location: Davis, CA

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Local realignements are helpful not because of sequencing quality concerns, but because of the general difficulty to get alignments right around indels, especially towards the end of reads .
Btw, just saw this nice paper:
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Old 08-20-2017, 10:55 AM   #3
Brian Bushnell
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I normally trim the first and last 5bp of reads for this reason (to avoid miscalled indels at the tips), after the reads are aligned. If you don't realign around indels, I recommend this. Might be a good idea even if you do realign; even with realignment, there are some features that you cannot resolve, since there is not enough information at the read tips.
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