vcfdist is a distance-based germline variant calling evaluation tool that:
- simultaneously evaluates SNPS, INDELs, and SVs up to 10Kb
- requires local phasing information for truth and query variants
- can standardize query and truth VCF variant representations
- can evaluate flip and switch phasing errors
vcfdist provides more accurate SNP, INDEL, and SV precision-recall curves than previous work, particularly when complex variants are involved.
This project is currently under active development. We welcome the submission of any feedback, issues, or suggestions for improvement! Check out the wiki for more information.
Please cite the following works if you use vcfdist:
[Nature Comms] vcfdist: Accurately benchmarking phased small variant calls in human genomes
@article{dunn2023vcfdist,
author={Dunn, Tim and Narayanasamy, Satish},
title={vcfdist: Accurately benchmarking phased small variant calls in human genomes},
journal={Nature Communications},
year={2023},
volume={14},
number={1},
pages={8149},
issn={2041-1723},
doi={10.1038/s41467-023-43876-x},
URL={https://doi.org/10.1038/s41467-023-43876-x}
}
[bioRxiv] Jointly benchmarking small and structural variant calls with vcfdist
@article{dunn2024vcfdist,
author={Dunn, Tim and Zook, Justin M and Holt, James M and Narayanasamy, Satish},
title={Jointly benchmarking small and structural variant calls with vcfdist},
journal={bioRxiv},
year={2024},
publisher={Cold Spring Harbor Laboratory},
doi={10.1101/2024.01.23.575922},
URL={https://doi.org/10.1101/2024.01.23.575922}
}
If you have conda installed with the bioconda channel (instructions here), run:
conda install vcfdistA pre-built Docker Hub image can be downloaded from here using:
sudo docker pull timd1/vcfdist
sudo docker run -it timd1/vcfdist:latest vcfdist --helpvcfdist is developed for Linux and its only dependencies are GCC v9.1+ and HTSlib v1.17. If you don't have HTSlib already, please set it up as follows:
> wget https://github.com/samtools/htslib/releases/download/1.17/htslib-1.17.tar.bz2
> tar -xvf htslib-1.17.tar.bz2
> cd htslib-1.17
> ./configure --prefix=/usr/local
> make
> sudo make install
> export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATHIf you do already have HTSlib installed elsewhere, make sure you've added it to your LD_LIBRARY_PATH, and that the HTSlib headers are included during compilation. At this point, installation is as simple as cloning the repository and building the executable. It should compile in less than one minute.
> git clone https://github.com/timd1/vcfdist
> cd vcfdist/src
> make
> sudo make install
> vcfdist --version
vcfdist v2.5.3The demo directory contains a demo script (shown below) and all required inputs. It operates on the first 5 million bases on chr1, and should run in about 3 seconds.
vcfdist \
query.vcf \
nist-v4.2.1_chr1_5Mb.vcf.gz \
GRCh38_chr1_5Mb.fa \
-b nist-v4.2.1_chr1_5Mb.bed \
-p results/ \
-v 0You can expect to see the following output:
PRECISION-RECALL SUMMARY
TYPE THRESHOLD TRUTH_TP QUERY_TP TRUTH_FN QUERY_FP PREC RECALL F1_SCORE F1_QSCORE
SNP NONE Q >= 0 8222 8222 1 2 0.9997 0.9998 0.9998 37.3885
SNP BEST Q >= 0 8222 8222 1 2 0.9997 0.9998 0.9998 37.3885
INDEL NONE Q >= 0 876 876 51 12 0.9864 0.9449 0.9652 14.5953
INDEL BEST Q >= 0 876 876 51 12 0.9864 0.9449 0.9652 14.5953
SV NONE Q >= 0 0 0 0 0 1.0000 1.0000 1.0000 100.000
SV BEST Q >= 0 0 0 0 0 1.0000 1.0000 1.0000 100.000
ALL NONE Q >= 0 9098 9098 52 14 0.9984 0.9943 0.9963 24.4200
ALL BEST Q >= 0 9098 9098 52 14 0.9984 0.9943 0.9963 24.4200
To include more details on intermediate results, run it again at higher verbosity by removing the -v 0 flag.
The vcfdist wiki has helpful information on command-line parameters, output documentation, and implementation.
This project is covered under the GNU GPL v3 license.
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