Closed skchronicles closed 2 months ago
Benchmarking command:
# Extract sample HG002 from the # multi-sample VCF, hap.py does # not support multi-sample VCFs # and our truthset is for HG002. module purge module load bcftools bcftools view \ -s HG002 \ snps_and_indels_recal_refinement_variants.vcf.gz \ -o HG002.snps_indels.haplotypecaller.recal.refined.vcf.gz \ -Oz # Run hap.py to evaluate the # performance of the new sub- # workflow & HaplotypeCaller. module purge module load singularity singularity run -B $PWD /path/to/hap.py_latest.sif \ /opt/hap.py/bin/hap.py \ --threads 12 \ -o HG002_benchmarking_results \ -r Homo_sapiens_assembly38.fasta \ -f truthset/HG002_GRCh38_1_22_v4.1_draft_benchmark.bed \ truthset/HG002_GRCh38_1_22_v4.1_draft_benchmark.vcf.gz \ HG002.snps_indels.haplotypecaller.recal.refined.vcf.gz
Benchmarking summary from hap.py:
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 526124 521041 5083 958334 5739 408419 1302 0.990339 0.989564 0.426176 0.989951 NaN NaN 1.528212 2.024520 INDEL PASS 526124 520564 5560 944090 4666 395693 1285 0.989432 0.991492 0.419126 0.990461 NaN NaN 1.528212 1.986641 SNP ALL 3365379 3339562 25817 3979159 37213 600838 4292 0.992329 0.988985 0.150996 0.990654 2.099711 1.952641 1.580978 1.745183 SNP PASS 3365379 3233487 131892 3521165 6736 279410 996 0.960809 0.997922 0.079352 0.979014 2.099711 2.053189 1.580978 1.618381
Results: Sample HG002
Benchmarking command:
Benchmarking summary from hap.py: