Workflow

TAPES Workflow using the provided toy dataset

Here you can find an example for workflow starting from a multi-sample VCF file and a fresh ANNOVAR download

Using ANNOVAR wrapping

First, cd to the main TAPES folder.

First use:
python3 tapes.py db -s -A /path/to/annovar/
To determine the ANNOVAR folder.

Then:
python3 tapes.py db -b --acmg
To download necessary databases (this might take some time).

Then:
python3 tapes.py annotate -i ./toy_dataset/toy_multi.vcf -o ./annotated_multi.vcf --acmg

To annotate the original vcf.

Then either:

• python3 tapes.py sort -i ./annotated_multi.vcf -o ./toy_report/ --tab

To prioritise the annotated vcf and generate the main output.

or

• python3 tapes.py sort -i ./annotated_multi.vcf -o ./toy_reports/ --tab --by_gene --by_sample --disease cancer --enrichr --list "TP53 BRCA1 BRCA2 PTEN KRAS" --trio ./toy_dataset/trio.txt --kegg "pathways in cancer"

To prioritise the annotated vcf, generate the main output and other few secondary reports

Without ANNOVAR WRAPPING

Try

• python3 tapes.py sort -i ./toy_dataset/toy_annovar_multi.vcf -o ./toy_report/ --tab

To prioritise the annotated vcf and generate the main output.

or

• python3 tapes.py sort -i ./toy_dataset/toy_vep_multi.vcf -o ./toy_reports/ --tab --by_gene --by_sample --disease cancer --enrichr --list "TP53 BRCA1 BRCA2 PTEN KRAS" --trio ./toy_dataset/trio.txt --kegg "pathways in cancer"

To prioritise the annotated vcf, generate the main output and other few secondary reports