Closed loverlyday closed 2 years ago
Hello @loverlyday
here you can find the 23 columns, which I extracted from the gnomAD vcf file and inserted into the SQL database.
Indeed, "AMR" is not part of it.
INFO=<ID=AF_amr,Number=A,Type=Float,Description="Alternate
allele frequency in samples of Latino ancestry">
1) You can recreate the SQL database by yourself by following these steps and including - AF_amr
here.
2) You can use AF_popmax
from the already existing SQL database to approximate the upper bound of the AF
Hello, I tried to follow these instructions to make a SQL database with additional population data. However, the Snakemake program only outputted createTSVtables.ipynb and 15G of .tsv.gz files (most of which "finished" at the same timestamp). It did not output the SQL database or insertVariants.ipynb. No errors were thrown, and there is space for the database to be made. How can I fix this? Thank you!
Hello @pkiehl2002,
Here you specify the location of the database: https://github.com/KalinNonchev/gnomAD_DB/blob/master/script_config.yaml By default it is: test_out
Can you find it there?
Please open an issue next time to continue the discussion as your problem is not related to the one above.
hello, when i use the gnomad_db_v3.1.2 ,i can't find the 'AMR' AF in the resluts, how can i get it from gnomad_db_v3.1.2 database?
thanks