xtmgah/admire

ADmiRE: Annotative Database of miRNA Elements

ADmiRE- Annotative Database of miRNA Elements

Types of Input files

Two primary ways of adding ADmiRE Annotations to existing list of variants and one way of calling miRNA region variants from BAM files:

1. Tab-separated Files (*.tsv, *.mafplus, etc.): Using Perl script in /ADmiRE/annotate_tsv_using_perl/

2. VCF Files: Using Ensembl Variant Effect Predictor (VEP) tool. Requires prior VEP installation, suitable for users with existing VEP workflows.

3. BAM Files: [COMING SOON]

Step-by-step Usage Guide

Clone the ADmiRE repository

git clone https://github.com/nroak/ADmiRE.git

Alternatively, you can download the ADmiRE directory in a ZIP file format. Make sure to save this file as "ADmiRE" and NOT "ADmiRE-master".

unzip ADmiRE.zip

To annotate a Tab separated file:

For Details, refer to ADmiRE/annotate_tsv_using_perl/README.md

cd ./ADmiRE/annotate_tsv_using_perl/

gzip -d ADmiRE.tab.gz

perl annoated_admire.pl --input INPUT_FILE --output OUTPUT_FILE

To annotate a VCF file:

For Details, refer to ADmiRE/annotate_VCF_using_VEP/README.md

cd ./ADmiRE/annotate_VCF_using_VEP

variant_effect_predictor.pl -i $input.vcf -o $input.admire.vcf --custom /path-to-file/ADmiRE.bed.gz,ADmiRE,bed,exact