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Unannotated VCF file

I just want to use the necessary ANNOVAR annotations for TAPES sorting

• Download ANNOVAR
• python3 tapes.py db -s -A /path/to/annovar/
• python3 tapes.py db -b --acmg --assembly hg19
• python3 tapes.py annotate -i /path/to/file.vcf -o /path/to/output.vcf --acmg -a hg19

I want to customise the ANNOVAR annotations used

• See detailed instructions on Database Management and Custom annotations

VEP or ANNOVAR annotated file

I want to sort and prioritise my annotated VCF file

• python3 tapes.py sort -i /to/annotated/file.vcf -o /to/output/folder/ --tab

I want to re-analyse TAPES main report

• python3 tapes.py analyse -i /to/main/report.txt -o /to/output/report.txt --single_option

Using the toy dataset

try:
python3 tapes.py sort -i ./toy_dataset/toy_annovar_multi.vcf -o ./Reports/ --tab --by_gene --by_sample --enrichr --list "MLH1 MSH6 MSH2" --disease "autosomal dominant" --kegg "pathways in cancer"