Column type set to VARCHAR(10) despite setting Type=Float in VCF file

[marivalen]

Good Afternoon,

I have the following line in my VCF file:

##INFO=<ID=gnomAD_exome_ALL,Number=1,Type=Float,Description="gnomAD_exome_ALL frequency annotation">

despite this what I see when I use db_info on a database created with vcf2db is:

variant_impacts gnomad_exome_all VARCHAR(10)

Is there any way to change this? Am I setting the type wrong? At the moment since that field is treated as a string I cannot make use to the frequency information to compare my variants.

Kind Regards,
Maria

[brentp]

can you show the full output of the vcf2db command that you used to create the database?

[marivalen]

The only thing besides the database that vcf2db outputs is:

/usr/lib/python2.7/dist-packages/sqlalchemy/sql/sqltypes.py:185: SAWarning: Unicode type received non-unicode bind param value '1'. (this warning may be suppressed after 10 occurrences) (util.ellipses_string(value),))
/usr/lib/python2.7/dist-packages/sqlalchemy/sql/sqltypes.py:185: SAWarning: Unicode type received non-unicode bind param value '2'. (this warning may be suppressed after 10 occurrences) (util.ellipses_string(value),))

Do you want me to also show what db_info returns on the database?

[brentp]

can you verify that you hvae the latest vcf2db? and if so, can you share a 1 line VCF so I can recreate the problem you are seeing?