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WGLab / InterVar

A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
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Issue with running example #87

Open rdutta1022 opened 1 year ago

rdutta1022 commented 1 year ago

Hi,

I am getting the following error when trying to run the example (with the following command: python3 Intervar.py -i example/ex1.avinput -o example/myanno). Would love any help in troubleshooting, thank you so much!

NOTICE: Running with system command <coding_change.pl example/myanno.refGene.exonic_variant_function.orig humandb/hg19_refGene.txt humandb/hg19_refGeneMrna.fa -alltranscript -out example/myanno.refGene.fa -newevf example/myanno.refGene.exonic_variant_function> Can't exec "coding_change.pl": No such file or directory at ./table_annovar.pl line 455. Error running system command: <coding_change.pl example/myanno.refGene.exonic_variant_function.orig humandb/hg19_refGene.txt humandb/hg19_refGeneMrna.fa -alltranscript -out example/myanno.refGene.fa -newevf example/myanno.refGene.exonic_variant_function> Warning: Customized disease cutoff 0.01 in config.ini, not suggested as 0.005 Warning: The InterVar seems not run correctly, please check your inputs , options and configure file! ERROR: The InterVar did not find the annotation result file from ANNOVAR! ERROR: The name of annotation result file should be like example/myanno*.hg19__multianno.txt

quanliustc commented 1 year ago

please download Annovar tool and put all the perl scripts in the InterVar folder