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Update OSS release doc for 1.8.0
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PiperOrigin-RevId: 700834501
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@kishwarshafin @copybara-github
kishwarshafin authored and copybara-github committed Nov 28, 2024
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8 changes: 4 additions & 4 deletions docs/deepvariant-xy-calling-case-study.md
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Expand Up @@ -138,8 +138,8 @@ Output:
```
Benchmarking Summary:
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al 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 24273 23457 816 30450 478 6100 28 359 0.966382 0.980370 0.200328 0.973326 NaN NaN 1.559454 0.070768
INDEL PASS 24273 23457 816 30450 478 6100 28 359 0.966382 0.980370 0.200328 0.973326 NaN NaN 1.559454 0.070768
SNP ALL 87443 86894 549 120732 776 33254 13 131 0.993722 0.991129 0.275437 0.992424 1.937122 1.630679 1.825434 0.050130
SNP PASS 87443 86894 549 120732 776 33254 13 131 0.993722 0.991129 0.275437 0.992424 1.937122 1.630679 1.825434 0.050130
INDEL ALL 24273 23289 984 31014 644 6687 49 465 0.959461 0.973527 0.215612 0.966443 NaN NaN 1.559454 0.068240
INDEL PASS 24273 23289 984 31014 644 6687 49 465 0.959461 0.973527 0.215612 0.966443 NaN NaN 1.559454 0.068240
SNP ALL 87443 86918 525 132164 1449 43958 11 234 0.993996 0.983573 0.332602 0.988757 1.937122 1.541799 1.825434 0.046716
SNP PASS 87443 86918 525 132164 1449 43958 11 234 0.993996 0.983573 0.332602 0.988757 1.937122 1.541799 1.825434 0.046716
```
120 changes: 60 additions & 60 deletions docs/trio-merge-case-study.md
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Expand Up @@ -115,7 +115,7 @@ serially is not the most effective approach.
```
N_SHARDS=$(nproc) # Or change to the number of cores you want to use
CAPTURE_BED=agilent_sureselect_human_all_exon_v5_b37_targets.bed
VERSION=1.7.0
VERSION=1.8.0
declare -a trio=(HG002 HG003 HG004)
for SAMPLE in "${trio[@]}"
Expand Down Expand Up @@ -226,12 +226,12 @@ The output is:
```
Checking: /data/deepvariant.cohort.vcf.gz
Family: [Sample_Diag-excap51-HG003-EEogPU + Sample_Diag-excap51-HG004-EEogPU] -> [Sample_Diag-excap51-HG002-EEogPU]
Concordance Sample_Diag-excap51-HG002-EEogPU: F:58162/58675 (99.13%) M:58574/58690 (99.80%) F+M:57946/58580 (98.92%)
Concordance Sample_Diag-excap51-HG002-EEogPU: F:46502/46866 (99.22%) M:46737/46863 (99.73%) F+M:46291/46785 (98.94%)
Sample Sample_Diag-excap51-HG002-EEogPU has less than 99.0 concordance with both parents. Check for incorrect pedigree or sample mislabelling.
828/58912 (1.41%) records did not conform to expected call ploidy
58818/58912 (99.84%) records were variant in at least 1 family member and checked for Mendelian constraints
187/58818 (0.32%) records had indeterminate consistency status due to incomplete calls
644/58818 (1.09%) records contained a violation of Mendelian constraints
584/47001 (1.24%) records did not conform to expected call ploidy
46959/47001 (99.91%) records were variant in at least 1 family member and checked for Mendelian constraints
129/46959 (0.27%) records had indeterminate consistency status due to incomplete calls
494/46959 (1.05%) records contained a violation of Mendelian constraints
```

From this report, we know that there is a 1.10% Mendelian violation rate, and
Expand All @@ -258,16 +258,16 @@ do
google/deepvariant:${VERSION} \
bcftools stats -f PASS \
${DIR}/${SAMPLE}.vcf.gz \
> ${DIR}/${SAMPLE}.stats
>> ${DIR}/${SAMPLE}.stats
done
```

| Sample | [3]ts | [4]tv | [5]ts/tv | [6]ts (1st | [7]tv (1st | [8]ts/tv (1st |
: : : : : ALT) : ALT) : ALT) :
| ------ | ----- | ----- | -------- | ---------- | ---------- | ------------- |
| HG002 | 29934 | 11684 | 2.56 | 29919 | 11665 | 2.56 |
| HG003 | 29808 | 11749 | 2.54 | 29795 | 11727 | 2.54 |
| HG004 | 30039 | 11850 | 2.53 | 30027 | 11833 | 2.54 |
| HG002 | 29955 | 11693 | 2.56 | 29942 | 11673 | 2.57 |
| HG003 | 29852 | 11769 | 2.54 | 29842 | 11746 | 2.54 |
| HG004 | 30048 | 11838 | 2.54 | 30037 | 11821 | 2.54 |

If you want to restrict to the truth BED files, use this command:

Expand All @@ -290,9 +290,9 @@ Which resulted in this table:
| Sample | [3]ts | [4]tv | [5]ts/tv | [6]ts (1st | [7]tv (1st | [8]ts/tv (1st |
: : : : : ALT) : ALT) : ALT) :
| ------ | ----- | ----- | -------- | ---------- | ---------- | ------------- |
| HG002 | 27704 | 10546 | 2.63 | 27696 | 10533 | 2.63 |
| HG003 | 27356 | 10514 | 2.60 | 27351 | 10502 | 2.60 |
| HG004 | 27491 | 10604 | 2.59 | 27484 | 10593 | 2.59 |
| HG002 | 27716 | 10549 | 2.63 | 27708 | 10536 | 2.63 |
| HG003 | 27382 | 10527 | 2.60 | 27378 | 10515 | 2.60 |
| HG004 | 27503 | 10607 | 2.59 | 27496 | 10596 | 2.59 |

### Rtg vcfstats

Expand All @@ -314,69 +314,69 @@ HG002:

```
Location : /data/HG002.vcf.gz
Failed Filters : 14598
Passed Filters : 45258
SNPs : 41584
Failed Filters : 14566
Passed Filters : 45290
SNPs : 41615
MNPs : 0
Insertions : 1867
Deletions : 1783
Indels : 22
Same as reference : 2
SNP Transitions/Transversions: 2.56 (41838/16338)
Total Het/Hom ratio : 1.49 (27087/18169)
SNP Het/Hom ratio : 1.51 (25017/16567)
Insertions : 1874
Deletions : 1779
Indels : 21
Same as reference : 1
SNP Transitions/Transversions: 2.56 (41843/16345)
Total Het/Hom ratio : 1.49 (27130/18159)
SNP Het/Hom ratio : 1.51 (25066/16549)
MNP Het/Hom ratio : - (0/0)
Insertion Het/Hom ratio : 1.08 (969/898)
Deletion Het/Hom ratio : 1.53 (1079/704)
Indel Het/Hom ratio : - (22/0)
Insertion/Deletion ratio : 1.05 (1867/1783)
Indel/SNP+MNP ratio : 0.09 (3672/41584)
Insertion Het/Hom ratio : 1.07 (967/907)
Deletion Het/Hom ratio : 1.53 (1076/703)
Indel Het/Hom ratio : - (21/0)
Insertion/Deletion ratio : 1.05 (1874/1779)
Indel/SNP+MNP ratio : 0.09 (3674/41615)
```

HG003:

```
Location : /data/HG003.vcf.gz
Failed Filters : 15423
Passed Filters : 45150
SNPs : 41519
Failed Filters : 15383
Passed Filters : 45190
SNPs : 41585
MNPs : 0
Insertions : 1851
Deletions : 1752
Indels : 21
Same as reference : 7
SNP Transitions/Transversions: 2.52 (41645/16537)
Total Het/Hom ratio : 1.48 (26923/18220)
SNP Het/Hom ratio : 1.50 (24879/16640)
Insertions : 1843
Deletions : 1743
Indels : 18
Same as reference : 1
SNP Transitions/Transversions: 2.52 (41678/16558)
Total Het/Hom ratio : 1.48 (26984/18205)
SNP Het/Hom ratio : 1.50 (24960/16625)
MNP Het/Hom ratio : - (0/0)
Insertion Het/Hom ratio : 1.11 (974/877)
Deletion Het/Hom ratio : 1.49 (1049/703)
Indel Het/Hom ratio : - (21/0)
Insertion/Deletion ratio : 1.06 (1851/1752)
Indel/SNP+MNP ratio : 0.09 (3624/41519)
Insertion Het/Hom ratio : 1.09 (962/881)
Deletion Het/Hom ratio : 1.49 (1044/699)
Indel Het/Hom ratio : - (18/0)
Insertion/Deletion ratio : 1.06 (1843/1743)
Indel/SNP+MNP ratio : 0.09 (3604/41585)
```

HG004:

```
Location : /data/HG004.vcf.gz
Failed Filters : 15166
Passed Filters : 45515
SNPs : 41857
Failed Filters : 15176
Passed Filters : 45505
SNPs : 41856
MNPs : 0
Insertions : 1859
Deletions : 1778
Indels : 20
Insertions : 1860
Deletions : 1766
Indels : 22
Same as reference : 1
SNP Transitions/Transversions: 2.55 (41671/16373)
Total Het/Hom ratio : 1.57 (27794/17720)
SNP Het/Hom ratio : 1.59 (25691/16166)
SNP Transitions/Transversions: 2.55 (41681/16348)
Total Het/Hom ratio : 1.57 (27795/17709)
SNP Het/Hom ratio : 1.59 (25703/16153)
MNP Het/Hom ratio : - (0/0)
Insertion Het/Hom ratio : 1.12 (983/876)
Deletion Het/Hom ratio : 1.62 (1100/678)
Indel Het/Hom ratio : - (20/0)
Insertion/Deletion ratio : 1.05 (1859/1778)
Indel/SNP+MNP ratio : 0.09 (3657/41857)
Insertion Het/Hom ratio : 1.11 (980/880)
Deletion Het/Hom ratio : 1.61 (1090/676)
Indel Het/Hom ratio : - (22/0)
Insertion/Deletion ratio : 1.05 (1860/1766)
Indel/SNP+MNP ratio : 0.09 (3648/41856)
```

### Run hap.py to calculate the accuracy of DeepVariant generated call sets
Expand Down Expand Up @@ -405,6 +405,6 @@ Accuracy F1 scores:

Sample | Indel | SNP
------ | -------- | --------
HG002 | 0.974074 | 0.993897
HG003 | 0.972967 | 0.993939
HG004 | 0.972967 | 0.993939
HG002 | 0.974037 | 0.994146
HG003 | 0.968448 | 0.993913
HG004 | 0.972569 | 0.994189

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