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Old 03-17-2012, 01:17 PM   #1
Location: boston

Join Date: Jun 2011
Posts: 27
Default unmapped vs soft-clipping

quite confused about this two terminology. I'm reading Pindel, the split-read algorithm. The author seems to make use of the information of "unmapped" reads. Also there are other split-read-based algorithm, which uses "soft-clipped" reads, which are the unaligned parts of reads.

In my eyes, the two look quite similar. Say we have a 100bp read, 50bp of which cannot map while the 50bp can. Then how would BWA categorize this read? Will BWA think this is "unmapped" read since 50bp cannot be mapped; or it's "mapped" but with 50bp "soft-clipped" sequences?

Or BWA has a scoring system for mapping, which sets a threshold for distinguishing the two?

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