Closed kcleal closed 2 years ago
No, we don't split reads. If we have a single read that crosses an SV then if it's only a little bit the end will get soft clipped, otherwise it probably won't get aligned.
From: Kez Cleal @.> Sent: Thursday, February 17, 2022 3:54 AM To: amplab/snap @.> Cc: Subscribed @.***> Subject: [amplab/snap] Supplementary mappings (Issue #152)
Hi, Thanks for the nice tool. Just a question - I was wondering if snap supports split-mappings a.k.a. supplementary alignments with a flag 2048? I can see from the documentation that secondary mappings can be output. Im interested in calling SVs and supplementary mappings are often very helpful for this purpose.
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Hi, Thanks for the nice tool. Just a question - I was wondering how snap chooses split-mappings a.k.a. supplementary alignments with a flag 2048? Is a minimum length of 50 bp used for example? How is the location of the supplementary alignment chosen - is it just based on the highest alignment score of candidate locations, or do the locations of the primary mappings influence the choice?