Skip to content

Instantly share code, notes, and snippets.

@williamrowell

williamrowell/HG002.giabv421.summary.csv

Last active June 6, 2022 06:05
Show Gist options
  • Save williamrowell/d902b6eaaa147eba53f1f4ab17532670 to your computer and use it in GitHub Desktop.
Save williamrowell/d902b6eaaa147eba53f1f4ab17532670 to your computer and use it in GitHub Desktop.
Download ZIP
Raw
deepvariant_v140_benchmarks.md

DeepVariant v1.4.0 Benchmarks for 35x PacBio HiFi

Sample Type METRIC.Recall METRIC.Precision METRIC.F1_Score
HG002 INDEL 99.40% 99.43% 99.41%
HG002 SNP 99.93% 99.97% 99.95%
HG003 INDEL 99.42% 99.45% 99.44%
HG003 SNP 99.91% 99.94% 99.93%
HG004 INDEL 99.41% 99.47% 99.44%
HG004 SNP 99.91% 99.96% 99.93%
Raw
HG002.giabv421.summary.csv
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 525467 522308 3159 1004238 3119 456981 1746 0.993988 0.994301 0.455052 0.994144 1.52827573414 2.00682078193
INDEL PASS 525467 522308 3159 1004238 3119 456981 1746 0.993988 0.994301 0.455052 0.994144 1.52827573414 2.00682078193
SNP ALL 3365126 3362716 2410 4365804 848 999299 476 0.999284 0.999748 0.228892 0.999516 2.10012756571 1.78797411801 1.58119585325 1.46169126378
SNP PASS 3365126 3362716 2410 4365804 848 999299 476 0.999284 0.999748 0.228892 0.999516 2.10012756571 1.78797411801 1.58119585325 1.46169126378
Raw
HG003.giabv421.summary.csv
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 504500 501591 2909 1000914 2906 475573 1660 0.994234 0.994468 0.475139 0.994351 1.48975928106 1.95700256217
INDEL PASS 504500 501591 2909 1000914 2906 475573 1660 0.994234 0.994468 0.475139 0.994351 1.48975928106 1.95700256217
SNP ALL 3327492 3324589 2903 4351366 1901 1022103 535 0.999128 0.999429 0.234892 0.999278 2.10257505008 1.78527966098 1.53513777165 1.43440937277
SNP PASS 3327492 3324589 2903 4351366 1901 1022103 535 0.999128 0.999429 0.234892 0.999278 2.10257505008 1.78527966098 1.53513777165 1.43440937277
Raw
HG004.giabv421.summary.csv
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 510518 507531 2987 1004232 2807 472407 1668 0.994149 0.994722 0.470416 0.994435 1.51613073552 2.00458945725
INDEL PASS 510518 507531 2987 1004232 2807 472407 1668 0.994149 0.994722 0.470416 0.994435 1.51613073552 2.00458945725
SNP ALL 3346600 3343539 3061 4382347 1437 1034433 571 0.999085 0.999571 0.236045 0.999328 2.10077981124 1.78566550082 1.58687160169 1.4816716066
SNP PASS 3346600 3343539 3061 4382347 1437 1034433 571 0.999085 0.999571 0.236045 0.999328 2.10077981124 1.78566550082 1.58687160169 1.4816716066
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment