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Old 09-12-2019, 06:57 AM   #2
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Location: Germany

Join Date: Oct 2008
Posts: 415

You don't mention any bioinformatics processes used, so it is impossible to answer your question.

What you mean is during the read mapping pipeline (FASTQ-> BAM).

We use NextSeq frequently and I would expect an indel of this size to be reliably detected using either single or paired end reads (PE always better).
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