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KalinNonchev / gnomAD_DB

This package scales the huge gnomAD files to a SQLite database, which is easy and fast to query. It extracts from a gnomAD vcf the minor allele frequency for each variant.
MIT License
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can't find 'AMR' AF in gnomad_db_v3.1.2 #19

Closed loverlyday closed 2 years ago

loverlyday commented 2 years ago

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

KalinNonchev commented 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

pkiehl2002 commented 1 year ago

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!

KalinNonchev commented 1 year ago

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?

KalinNonchev commented 1 year ago

Please open an issue next time to continue the discussion as your problem is not related to the one above.