_Record attributes for variant type and sub_type

[arq5x]

I think it would be very helpful to add attributes to the _Record API that report:

1. The variant type (e.g., "snp", "indel", "sv").
2. The variant sub_type:
   • if variant == "snp"
     "ts" for transition
     "tv" for transversion
   • if variant == "indel"
     "del" for deletion
     "ins" for insertion

etc.

If you are open to this, I have some existing code for this that I could incorporate.

[jamescasbon]

On Wed, Jan 25, 2012 at 2:28 PM, Aaron Quinlan <
reply@reply.github.com

wrote:

I think it would be very helpful to add attributes to the _Record API
that report:

1. The variant type (e.g., "snp", "indel", "sv").
2. The variant sub_type:
   • if variant == "snp"
     "ts" for transition
     "tv" for transversion
   • if variant == "indel"
     "del" for deletion
     "ins" for insertion

etc.

If you are open to this, I have some existing code for this that I could
incorporate.

Sounds good, but would have to be a list since a Record can have multiple
variants, i.e. ALT=['A','.'] is a SNP and a DEL.

I actually would like to have a parse mode where each Record can only have
one variant - would make all this much easier.

[arq5x]

Yep, a list would be needed in the current framework. How would you propose to handle genotypes representing the different alleles were you to expand multi-allelic variants into discrete Records?

[jamescasbon]

Is this now a duplicate of #31? I think so.