Validation and benchmarking with A-full and CPCG0196-B1 - single WGS mode
Summary tables comparing call-gSNP v7.0.0 to call-gSNP-DSL1 v5.4.5
Input: /hot/pipeline/development/slurm/call-gSNP/7.0.0-rc1/pre_standardization/single_A-full/A-full.csv
- call-gSNP v7.0.0:
/hot/pipeline/development/slurm/call-gSNP/7.0.0-rc1/pre_standardization/single_A-full- Runtime: 2d 4h 14m 2s
- call-gSNP-DSL1 v5.4.5:
/hot/pipeline/development/slurm/call-gSNP/DSL1_outputs/v5.4.5_for_comparison- Runtime: 2d 15h 9m 53s
Raw VCF comparison:
| Version | VCF (Common) | VCF (Unique) |
|---|---|---|
| 7.0.0 | 4813793 | 74 (0.0015%) |
| DSL1-5.4.5 | 4813793 | 62 (0.0013%) |
Raw GVCF comparison:
| Version | VCF (Common) | VCF (Unique) |
|---|---|---|
| 7.0.0 | 51962094 | 3234 (0.0062%) |
| DSL1-5.4.5 | 51962094 | 3454 (0.0066%) |
Filtered SNV GVCF:
| Version | VCF (Common) | VCF (Unique) |
|---|---|---|
| 7.0.0 | 3265039 | 24550 (0.74%) |
| DSL1-5.4.5 | 3265039 | 17728 (0.54%) |
Filtered INDEL GVCF:
| Version | VCF (Common) | VCF (Unique) |
|---|---|---|
| 7.0.0 | 811214 | 2875 (0.35%) |
| DSL1-5.4.5 | 811214 | 6501 (0.79%) |
Realigned and recalibrated BAM:
| SAMPLE | LEFT_FILE | RIGHT_FILE | MAPPINGS_MATCH | MAPPINGS_DIFFER | UNMAPPED_BOTH | UNMAPPED_LEFT | UNMAPPED_RIGHT | MISSING_LEFT | MISSING_RIGHT | DUPLICATE_MARKINGS_DIFFER | ARE_EQUAL |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Normal | DSL1-5.4.5 | 7.0.0 | 1723823909 | 11 | 4585406 | 0 | 0 | 3753 | 0 | 0 | N |
Summary tables comparing call-gSNP v7.0.0 to call-gSNP-DSL1 v5.4.3
Input: /hot/pipeline/development/slurm/call-gSNP/7.0.0-rc1/pre_standardization/single_CPCG0196-B1/CPCG0196-B1.csv
- call-gSNP v7.0.0:
/hot/pipeline/development/slurm/call-gSNP/7.0.0-rc1/pre_standardization/single_CPCG0196-B1- Runtime: 2d 13h 30m 29s
- call-gSNP-DSL1 v5.4.3:
/hot/pipeline/development/slurm/call-gSNP/DSL1_outputs/call-gSNP_v5.4.3/outputs_CPCG0196-B1/call-gSNP-20210324-210359/- Runtime: 3d 0h 9m 53s
Raw VCF comparison:
| Version | VCF (Common) | VCF (Unique) |
|---|---|---|
| 7.0.0 | 4863231 | 133768 (2.68%) |
| DSL1-5.4.3 | 4863231 | 577 (0.012%) |
Raw GVCF comparison:
| Version | VCF (Common) | VCF (Unique) |
|---|---|---|
| 7.0.0 | 51588596 | 3653326 (6.61%) |
| DSL1-5.4.3 | 51588596 | 7506 (0.014%) |
Filtered SNV GVCF:
| Version | VCF (Common) | VCF (Unique) |
|---|---|---|
| 7.0.0 | 3035126 | 130500 (4.02%) |
| DSL1-5.4.3 | 3035126 | 77095 (2.38%) |
Filtered INDEL GVCF:
| Version | VCF (Common) | VCF (Unique) |
|---|---|---|
| 7.0.0 | 844167 | 6042 (0.71%) |
| DSL1-5.4.3 | 844167 | 361 (0.042%) |
Realigned and recalibrated BAM:
| SAMPLE | LEFT_FILE | RIGHT_FILE | MAPPINGS_MATCH | MAPPINGS_DIFFER | UNMAPPED_BOTH | UNMAPPED_LEFT | UNMAPPED_RIGHT | MISSING_LEFT | MISSING_RIGHT | DUPLICATE_MARKINGS_DIFFER | ARE_EQUAL |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Normal | DSL1-5.4.3 | 7.0.0 | 1935641125 | 182 | 16050267 | 0 | 0 | 21372 | 0 | 0 | N |