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philres / ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
MIT License
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Explaination of SV Tag? #18

Closed dantaki closed 7 years ago

dantaki commented 7 years ago

The documentation for the SV tag is sparse. I noticed it's used for Sniffles, but I was wondering if I could have some more information about this tag, for example what does the signed integer following the tag indicate?

Is it the number of Supplementary Alignments for a given read? Thanks for the response.

philres commented 7 years ago

Hi!

The SV tag is a bit flag we use for communication between ngmlr and sniffle. The first bit is set if a read was clipped because of Ns in the reference sequence.

Please, let me know if you need any additional tags.

Thanks, Philipp