OpenOmics/genome-seek

Benchmarking germline pipeline for accuracy and precision after completion

skchronicles opened this issue · 2 comments

skchronicles commented
Benchmarking germline pipeline for accuracy and precision after completion
skchronicles commented

Results: Sample HG002

Benchmarking command:

module load singularity
singularity run --bind $PWD /path/to/hap.py_latest.sif  \
    /opt/hap.py/bin/hap.py \
        --threads 24 \
        -o HG002_genome_seek \
        -r Homo_sapiens_assembly38.fasta \
        -f HG002/HG002_GRCh38_1_22_v4.1_draft_benchmark.bed \ 
        HG002/HG002_GRCh38_1_22_v4.1_draft_benchmark.vcf.gz \
       deepvariant/VCFs/HG002.germline.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    521450      4674       900211      1291     354413    247       0.991116          0.997635        0.393700         0.994365                     NaN                     NaN                   1.528212                   1.944087
 INDEL   PASS       526124    521431      4693       899474      1281     353704    247       0.991080          0.997653        0.393234         0.994356                     NaN                     NaN                   1.528212                   1.942003
   SNP    ALL      3365379   3342074     23305      3733872      2338     387259   1031       0.993075          0.999301        0.103715         0.996178                2.099711                2.018322                   1.580978                   1.528736
   SNP   PASS      3365379   3342068     23311      3733844      2338     387232   1031       0.993073          0.999301        0.103709         0.996178                2.099711                2.018343                   1.580978                   1.528717
skchronicles commented

More information/examples about benchmarking performance can be on here:
https://github.com/google/deepvariant/blob/r1.3/docs/deepvariant-quick-start.md