Closed zainomarali closed 4 months ago
from gnomad_db.database import gnomAD_DB
db = gnomAD_DB(db_loc, gnomad_version="v4")
db.get_info_from_str("12:47818936:C>T", "*")
chrom 12
pos 47818936
ref C
alt T
filter PASS
AC 19849.0
AN 152188.0
AF 0.130424
MQ 59.9972
QD 15.3561
ReadPosRankSum 0.381
VarDP 1311211.0
AS_VQSLOD 22.0502
AC_grpmax 13083.0
AN_grpmax 67972.0
AF_grpmax 0.192476
AF_eas 0.005803
AF_nfe 0.192476
AF_fin 0.174008
AF_afr 0.039115
AF_asj 0.15562
Name: 0, dtype: object
Hi, it looks like your variant is available in the WGS version v4. Please make sure that the WGS v4 sqlite database name is gnomad_db.sqlite3
Hi,
I looked up 371 variants in your v4 gnomad sqlite database (downloaded using this link: "https://zenodo.org/records/10066323/files/gnomad_db_wgs_v4.0.sqlite3.gz?download=1", and then followed your instructions to download and unzip in python).
I converted my variants to strings of the form "8:56113670:C>A" and then used "get_info_from_str" to extract the info. 96 variants fail to return values (I am attaching the variants here).
missingvars_sqlite.txt
Not sure what the issue is, when I search by region I am also unable to extract the info, even though all the information for these variants is available on the gnomAD website. I would really like to avoid having to download the VCF files if possible and your tool seemed to be the best way.
Thank you for your help.