diff --git a/docs/metrics.md b/docs/metrics.md index 73a6e186..12f7c281 100644 --- a/docs/metrics.md +++ b/docs/metrics.md @@ -15,7 +15,7 @@ total | 431m = 6.7 hours ### Accuracy -hap.py results on HG002 (all chromosomes). +hap.py results on HG002 (all chromosomes), using NIST v4.2 truth. Type | # TP | # FN | # FP | Recall | Precision | F1_Score ----- | ------- | ----- | ---- | -------- | --------- | -------- @@ -38,7 +38,7 @@ total | 21m ### Accuracy -hap.py results on HG002 (all chromosomes). +hap.py results on HG002 (all chromosomes), using NIST v4.1 truth. Type | # TP | # FN | # FP | Recall | Precision | F1_Score ----- | ------- | ---- | ---- | -------- | --------- | -------- @@ -48,6 +48,8 @@ SNP | 38180 | 396 | 116 | 0.989735 | 0.996975 | 0.993341 ## PacBio (HiFi) +### Runtime + Runtime is on HG002 (all chromosomes). Stage | Time (minutes) @@ -59,7 +61,7 @@ total | 421 = 7 hours ### Accuracy -hap.py results on HG002 (chr20). +hap.py results on HG002 (chr20), using NIST v4.2 truth. (The input BAM is haplotagged already and DeepVariant was run with `--sort_by_haplotypes=true --parse_sam_aux_fields=true`.) @@ -84,8 +86,8 @@ total | 455 m = 7.6 hours ### Accuracy -Evaluating on HG003 (all chromosomes), which was held out while training the -hybrid model. +Evaluating on HG003 (all chromosomes, using NIST v4.2 truth), which was held out +while training the hybrid model. Type | # TP | # FN | # FP | Recall | Precision | F1_Score ----- | ------- | ---- | ---- | -------- | --------- | --------