Compare VCFs using illumina hap.py and nextflow
docker pull pkrusche/hap.py:v0.3.9
singularity build hap.py_v0.3.9.img docker:https://pkrusche/hap.py:v0.3.9 (if prefer singularity)
git clone https://github.com/oxfordfun/vcfcompare
nextflow run compare.nf -profile docker
--input tests/input (folder with vcf files to be compared against the truevcf)
--ref tests/tests/ref/NC_000962.fasta (reference used for vcf generation)
--refindex tests/ref/NC_000962.fasta.fai (indexed reference by samtools)
--refvcf tests/ref/snps.vcf (true vcf to compare against)
tests/ref/snps.vcf (a vcf generated by [snippy](https://github.com/tseemann/snippy) as true vcf)
tests/input/snps-test-0.vcf (same as snps.vcf)
tests/input/snps-test-1.vcf (one mutation made)
tests/input/snps-test-2.vcf (two mutations made)
| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| INDEL | ALL | 120 | 120 | 0 | 120 | 0 | 0 | 0 | 1.0 | 1.0 | 0.0 | 1.0 | 0.0 | 0.0 | ||
| INDEL | PASS | 120 | 120 | 0 | 120 | 0 | 0 | 0 | 1.0 | 1.0 | 0.0 | 1.0 | 0.0 | 0.0 | ||
| SNP | ALL | 1356 | 1356 | 0 | 1356 | 0 | 0 | 0 | 1.0 | 1.0 | 0.0 | 1.0 | 1.66404715128 | 1.66404715128 | 0.0 | 0.0 |
| SNP | PASS | 1356 | 1356 | 0 | 1356 | 0 | 0 | 0 | 1.0 | 1.0 | 0.0 | 1.0 | 1.66404715128 | 1.66404715128 | 0.0 | 0.0 |
| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| INDEL | ALL | 120 | 120 | 0 | 120 | 0 | 0 | 0 | 1.0 | 1.0 | 0.0 | 1.0 | 0.0 | 0.0 | ||
| INDEL | PASS | 120 | 120 | 0 | 120 | 0 | 0 | 0 | 1.0 | 1.0 | 0.0 | 1.0 | 0.0 | 0.0 | ||
| SNP | ALL | 1356 | 1355 | 1 | 1356 | 1 | 0 | 0 | 0.999263 | 0.999263 | 0.0 | 0.999263 | 1.66404715128 | 1.66404715128 | 0.0 | 0.0 |
| SNP | PASS | 1356 | 1355 | 1 | 1356 | 1 | 0 | 0 | 0.999263 | 0.999263 | 0.0 | 0.999263 | 1.66404715128 | 1.66404715128 | 0.0 | 0.0 |
| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| INDEL | ALL | 120 | 120 | 0 | 120 | 0 | 0 | 0 | 1.0 | 1.0 | 0.0 | 1.0 | 0.0 | 0.0 | ||
| INDEL | PASS | 120 | 120 | 0 | 120 | 0 | 0 | 0 | 1.0 | 1.0 | 0.0 | 1.0 | 0.0 | 0.0 | ||
| SNP | ALL | 1356 | 1354 | 2 | 1356 | 2 | 0 | 0 | 0.998525 | 0.998525 | 0.0 | 0.998525 | 1.66404715128 | 1.65882352941 | 0.0 | 0.0 |
| SNP | PASS | 1356 | 1354 | 2 | 1356 | 2 | 0 | 0 | 0.998525 | 0.998525 | 0.0 | 0.998525 | 1.66404715128 | 1.65882352941 | 0.0 | 0.0 |