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shishenyxx / DeepMosaic

DeepMosaic is a deep-learning-based mosaic single nucleotide classification tool without the need of matched control information.
https://www.nature.com/articles/s41587-022-01559-w
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different gnomad databases? #17

Closed apaul7 closed 11 months ago

apaul7 commented 11 months ago

Hello! Thank you for making this program! I believe that the the hg19/hg38 gnomad annotations are somewhat hardcoded into the program. Specifically to v2.0.1, which for hg38 is installed with annovar at hg38_ gnomad_genome.txt. I only have the newer versions of gnomad downloaded in my annovar installation.

Could you create an input option to control what version of gnomad is used for annotations? I got around the error:

Error: the database file /annovar/annovar/humandb/hg38_gnomad_genome.txt is not present

by symlinking hg38_gnomad312_genome.txt to hg38_ gnomad_genome.txt. Which works but is not an ideal solution.

shishenyxx commented 11 months ago

Option added and the tutorial and singularity will be updated. We will release a new subversion. Thank you so much for your feedback!

Best,

Arzoo and Xiaoxu