Only a small percentage of SNVs receiving annotation using offline tool

kircherlab / CADD-scripts

CADD scripts release for offline scoring. For more information about CADD, please visit our website

http://cadd.gs.washington.edu

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Only a small percentage of SNVs receiving annotation using offline tool #36

Closed jessicabonnie closed 2 years ago

jessicabonnie commented 3 years ago

Hello, I have attached markdown output where I have done my best to illustrate and debug the issue I am having where the annotated output file only contains annotation for a small number of SNVs and the rest only these columns: Chr, Pos, A1, A2, RawScore, PHRED. CADD_debug_08042021.pdf

makirc commented 3 years ago

Hi there, as you suspect in your detailed report, having a file without annotations in your "incl_anno" folder is the problem. Please move /scratch/groups/abattle4/jessica/RareVar_AFR/cadd/CADD-scripts/data/prescored/GRCh38_v1.6/incl_anno/gnomad.genomes.r3.0.snv.tsv.gz to another folder and please try again. Best, Martin