Supplementary mappings
kcleal opened this issue · 1 comments
kcleal commented
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?
bolosky commented
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.
-
Reply to this email directly, view it on GitHub<https://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Famplab%2Fsnap%2Fissues%2F152&data=04%7C01%7Cbolosky%40microsoft.com%7Ca86e52e54d9843a2465a08d9f20c3e67%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C637806956681331651%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=iDy7xZc1mZtqUK1v90FVWjO%2FZ2PVQBTCyRGoO4EHooU%3D&reserved=0>, or unsubscribe<https://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAAHPTWL5UVMLAVAYKLWHCTDU3TOXBANCNFSM5OUOOXEQ&data=04%7C01%7Cbolosky%40microsoft.com%7Ca86e52e54d9843a2465a08d9f20c3e67%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C637806956681331651%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=DdWtoE3W13WgoQ9o3LHURFnmDN2Clmjw5bxA%2FTdTx%2Bg%3D&reserved=0>.
Triage notifications on the go with GitHub Mobile for iOS<https://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7Cbolosky%40microsoft.com%7Ca86e52e54d9843a2465a08d9f20c3e67%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C637806956681331651%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=quvqb5wYqQTtqb8bnmqKGKzCnFZ0YJdFIeN9azoK8bA%3D&reserved=0> or Android<https://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7Cbolosky%40microsoft.com%7Ca86e52e54d9843a2465a08d9f20c3e67%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C637806956681331651%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=R9HMxap7DAdfWgseCs2L%2B%2F788FKzRA1uTs8IVSRGESI%3D&reserved=0>.
You are receiving this because you are subscribed to this thread.Message ID: ***@***.******@***.***>>