Entering edit mode
2.3 years ago
Merlin
•
0
How can I use the MitImpact3.1.0 database in Annovar? It seems to be that only MitImpact2 was available in Annovar. I downloaded the MitImpact3.1.0 database manually, and tried the following code to build the database but failed;
(base) Server:~/software/annovar$ annotate_variation.pl -buildver hg38 MitImpact_db_3.1.0.txt humandb/
NOTICE: The --geneanno operation is set to ON by default
NOTICE: Output files are written to MitImpact_db_3.1.0.txt.variant_function, MitImpact_db_3.1.0.txt.exonic_variant_function
NOTICE: Reading gene annotation from humandb/hg38_refGene.txt ... Done with 88819 transcripts (including 21511 without coding sequence annotation) for 28307 unique genes
NOTICE: Variants with invalid input format are written to MitImpact_db_3.1.0.txt.invalid_input
Since previous title ("Postdoc") had no relation to the question I changed the title of the post to reflect the content.