RecallME: a tool for VCF files comparison and efficient validation method

RecallME is a containerized python tool for VCF file comparison and variant calling pipelines benchmarking and optimization.

Quick start

To run RecallME you need to activate the conda environment and to install singularity (> v.3) and ANNOVAR (it requires a license free of charge for non-commercial purposes). For more information about ANNOVAR, please visit the <a href="https://annovar.openbioinformatics.org/en/latest/" target="_blank"> official website</a>

Installation and setup

To start using RecallME v.0.2, type the following commands:

git clone https://github.com/mazzalab-ieo/recallme.git
cd recallme/
conda env create --file env.txt --name {name_env}

Basic commands

To run a comparison, type:

python RecallME.py -q $QUERY_VCF \
--high_conf_bed $BED \
--query_format VCF \
-g $GROUND_TRUTH \
--gt_format VCF \
-f $FASTA \
--genome_bed $GENOME_BED \
-b $BAM \
-a $ANNOVAR_DIR \
-o $OUT_DIR \
--caller $CALLER_NAME 

• GENOME_BED is a bedtools specific bed file with chromosome sizes in bps (i.e. chr1 n) or a .fai index.
• BAM file for query
• ANNOVAR_DIR the directory where is stored convert2annovar.pl which is required for running RecallME
• CALLER_NAME the name of the caller used to produce the query VCF file (GATK, TVC, Deepvariant, VarScan, LoFreq)

For more info on required and not required commands, please type:

python RecallME.py --help

Tutorial

To run the example, open a terminal and type:

conda activate {name_env}
cd recallme/
#add the annovar folder within run_example.sh
bash run_example.sh

<code>run_example.sh</code> produces an outdir/ folder in the run_example/ directory as follows:<br>

<img src="www/diag.png" alt="diag" width="500" height="333">

After the output has been generated, go to the <a href="https://translational-oncology-lab.shinyapps.io/recallme/" target="_blank">web app</a> and load the AVinputs (query_split_var_type.avinput + ground_truth_var_type.avinput) and the rds object to visualize your results and to optimize your pipeline.

For additional information, please check the <a href="https://translational-oncology-lab.shinyapps.io/recallme/" target="_blank">about</a> page for interrogating the manual.

License

RecallME is under MIT License. BEDTOOLS is under GNU General Public License.

Citations

If you use RecallME in a scientific article, please cite: G Vozza, E Bonetti, G Tini, V Favalli, G Frige’, G Bucci, S De Summa, M Zanfardino, F Zapelloni, L Mazzarella, Benchmarking and improving the performance of variant-calling pipelines with RecallME, Bioinformatics, 2023; <a href="https://doi.org/10.1093/bioinformatics/btad722" target="_blank" > doi: https://doi.org/10.1093/bioinformatics/btad722 </a>