Daniel Cameron

The question of the most appropriate license will need to be resolved. MIT since it covers both software and documentation? MIT+CC-BY-SA? Other options?

This issue should be resolved before we start pushing SAM and VCF files to the official suite of test case/examples.

My interpretation is also a) since if filters were applied, then the spec provides `PASS` as a special value to indicate as such (but it does not explicitly require this)....

>then we need an official tag for describing where the list of secondary alignments are, or at least where the template-specific RNEXT/PNEXT/TLEN figures are for this secondary alignment Isn't this...

If this feature is designed to support somatic samples, shouldn't we include support for subclone at the same time? Currently everything is designed around pure samples with integer copy numbers...

Seems reasonable. We'd have to make CN a float instead of a int but that's forr aanother PR.

> Also, a lot of the talk on this page is with regards to somatic variation. The use-case we want this for is simpler: 2/1 calls of X chromosomes and...

circular/linear is already covered in the `@SG` `TP` field.

Are we planning to fix the cardinality of SV fields in this PR? About half the SV fields assume one SV per loci, and the other half don't. See #133

@thefferon inverted duplication example added to confluence