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| # VCFCompare | ||
| A Python program for evaluating site-level concordance of a query VCF against a truth VCF. | ||
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| This tool compares two variant callsets against each other and produces a CSV file with summary metrics. The summary metric CSV file contains: | ||
| The summary metric CSV file contains: | ||
| * Variant type: SNV or INDEL | ||
| * Total number of variants in the truth and query VCF files | ||
| * Total true-positive, false-positive, and false-negative calls | ||
| * Recall and Precision | ||
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| ## Usage | ||
| This tool compares two variant callsets against each other and produces a CSV file with summary metrics. | ||
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| In the following examples, we assume that the code has been installed to the directory `${VCFCompare}`. | ||
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| ```bash | ||
| $ python3 ${VCFCompare}/src/python/VCFCompare.py \ | ||
| -t example/gatk_variants.vcf \ | ||
| -q bcftools_variants.vcf \ | ||
| -o output | ||
| $ ls test.* | ||
| test.csv | ||
| ``` | ||
| python3 VCFCompare.py --truth truth.vcf --query query.vcf --output output | ||
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| The example above compares an example run of GATK 4.1.0.0 against an example run of bcftools 1.9 on the same random sample. | ||
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| The summary metric CSV file contains: | ||
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| Type | TRUTH.TOTAL | TP | FP | FN | QUERY.TOTAL | Recall | Precision | ||
| --- | --- | --- | --- | --- | --- | --- | --- | ||
| SNV | 3610 | 3573 | 538 | 37 | 4111 | 0.989750693 | 0.869131598 | ||
| INDEL | 205 | 104 | 101 | 101 | 247 | 0.507317073 | 0.421052632 | ||
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| ##Upset Plots | ||
| If you want to visualize the difference and intersection between the truth and query VCF files, you can use the upset.R script under src/R/ | ||
| The upset.R script runs on a set of VCFCompare.py results produced with the -o flag, as shown in the example above | ||
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| ```bash | ||
| $ Rscript ${VCFCompare}/src/R/upset.R \ | ||
| -i test.csv \ | ||
| -o TestRun | ||
| $ ls TestRun.* | ||
| TestRun.INDEL.pdf TestRun.SNV.pdf | ||
| ``` | ||
| This will produce two PDF files: one for SNVs and one for INDELs. | ||
| Below is a screenshot for SNVs | ||
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