| Data | Tool | SNP | Indel | ||
| FDR | FNR | FDR | FNR | ||
| WES | Ensembl 2of4 (bcbio 1.1.2) | 0.22% | 0.23% | 7.41% | 5.98% |
| WGS | Gatk 4.0.12.0 (bcbio) | 0.10% | 0.12% | 0.95% | 1.19% |
Data:
| Sample name | NA12878 |
|---|---|
| Cycles | 2x100 |
| Avg coverage for Ensembl protein coding exons | 156 |
| Median bp coverage for Ensembl protein coding exons | 162 |
| Reads (single) | 142,641,214 |
| Insert size | 190 |
Methods: I intersect callable regions from bcbio x giab bed file x capture kit bed file = 50,436,223 bp in my case. It includes some non-coding sites, coding only should be 30M. Then I use RTG to report baseline-TP, FP, FN. My bcbio config:
details:
- algorithm:
aligner: bwa
effects: false
ensemble:
numpass: 2
use_filtered: false
mark_duplicates: true
realign: false
recalibrate: false
remove_lcr: false
save_diskspace: true
tools_off:
- vqsr
tools_on:
- noalt_calling
variantcaller:
- gatk-haplotype
- freebayes
- platypus
- samtools
validate: giab-NA12878/truth_small_variants.vcf.gz
validate_regions: giab-NA12878/truth_regions.bed
Results:
SNPs:
| variant caller | gatk 4.0.12.0 | gatk 4.0.1.2 | freebayes 1.1.0.46 | ensemble |
|---|---|---|---|---|
| tp | 38,614 | 38,627 | 38,649 | 38,625 |
| fp | 203 | 211 | 285 | 266 |
| fn | 129 | 116 | 94 | 91 |
| FDR | 0.52% | 0.54% | 0.73% | 0.68% |
| FNR | 0.33% | 0.30% | 0.24% | 0.23% |
| Target | 38743 | 38743 | 38743 | 38743 |
Indels:
| variant caller | gatk 4.0.12.0 | gatk 4.0.1.2 | freebayes 1.1.0.46 | ensemble |
|---|---|---|---|---|
| tp | 2874 | 2883 | 2776 | 2855 |
| fp | 364 | 384 | 238 | 228 |
| fn | 170 | 161 | 268 | 189 |
| FDR | 11.24% | 11.75% | 7.90% | 7.40% |
| FNR | 5.58% | 5.29% | 8.80% | 6.21% |