Comments (3)
On Wed, Jan 25, 2012 at 2:28 PM, Aaron Quinlan <
[email protected]
wrote:
I think it would be very helpful to add attributes to the
_Record
API
that report:
- The variant type (e.g., "snp", "indel", "sv").
- The variant sub_type:
- if variant == "snp"
"ts" for transition
"tv" for transversion- if variant == "indel"
"del" for deletion
"ins" for insertionetc.
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.
from pyvcf.
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?
from pyvcf.
Is this now a duplicate of #31? I think so.
from pyvcf.
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