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Update OSS release doc for 1.8.0
PiperOrigin-RevId: 700834501
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‎docs/deepvariant-xy-calling-case-study.md

+4-4
Original file line numberDiff line numberDiff line change
@@ -138,8 +138,8 @@ Output:
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```
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Benchmarking Summary:
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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
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INDEL ALL 24273 23457 816 30450 478 6100 28 359 0.966382 0.980370 0.200328 0.973326 NaN NaN 1.559454 0.070768
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INDEL PASS 24273 23457 816 30450 478 6100 28 359 0.966382 0.980370 0.200328 0.973326 NaN NaN 1.559454 0.070768
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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
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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
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INDEL ALL 24273 23289 984 31014 644 6687 49 465 0.959461 0.973527 0.215612 0.966443 NaN NaN 1.559454 0.068240
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INDEL PASS 24273 23289 984 31014 644 6687 49 465 0.959461 0.973527 0.215612 0.966443 NaN NaN 1.559454 0.068240
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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
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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
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```

‎docs/trio-merge-case-study.md

+60-60
Original file line numberDiff line numberDiff line change
@@ -115,7 +115,7 @@ serially is not the most effective approach.
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```
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N_SHARDS=$(nproc) # Or change to the number of cores you want to use
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CAPTURE_BED=agilent_sureselect_human_all_exon_v5_b37_targets.bed
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VERSION=1.7.0
118+
VERSION=1.8.0
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declare -a trio=(HG002 HG003 HG004)
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for SAMPLE in "${trio[@]}"
@@ -226,12 +226,12 @@ The output is:
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```
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Checking: /data/deepvariant.cohort.vcf.gz
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Family: [Sample_Diag-excap51-HG003-EEogPU + Sample_Diag-excap51-HG004-EEogPU] -> [Sample_Diag-excap51-HG002-EEogPU]
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Concordance Sample_Diag-excap51-HG002-EEogPU: F:58162/58675 (99.13%) M:58574/58690 (99.80%) F+M:57946/58580 (98.92%)
229+
Concordance Sample_Diag-excap51-HG002-EEogPU: F:46502/46866 (99.22%) M:46737/46863 (99.73%) F+M:46291/46785 (98.94%)
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Sample Sample_Diag-excap51-HG002-EEogPU has less than 99.0 concordance with both parents. Check for incorrect pedigree or sample mislabelling.
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828/58912 (1.41%) records did not conform to expected call ploidy
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58818/58912 (99.84%) records were variant in at least 1 family member and checked for Mendelian constraints
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187/58818 (0.32%) records had indeterminate consistency status due to incomplete calls
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644/58818 (1.09%) records contained a violation of Mendelian constraints
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584/47001 (1.24%) records did not conform to expected call ploidy
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46959/47001 (99.91%) records were variant in at least 1 family member and checked for Mendelian constraints
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129/46959 (0.27%) records had indeterminate consistency status due to incomplete calls
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494/46959 (1.05%) records contained a violation of Mendelian constraints
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```
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From this report, we know that there is a 1.10% Mendelian violation rate, and
@@ -258,16 +258,16 @@ do
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google/deepvariant:${VERSION} \
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bcftools stats -f PASS \
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${DIR}/${SAMPLE}.vcf.gz \
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> ${DIR}/${SAMPLE}.stats
261+
>> ${DIR}/${SAMPLE}.stats
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done
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```
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| Sample | [3]ts | [4]tv | [5]ts/tv | [6]ts (1st | [7]tv (1st | [8]ts/tv (1st |
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: : : : : ALT) : ALT) : ALT) :
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| ------ | ----- | ----- | -------- | ---------- | ---------- | ------------- |
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| HG002 | 29934 | 11684 | 2.56 | 29919 | 11665 | 2.56 |
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| HG003 | 29808 | 11749 | 2.54 | 29795 | 11727 | 2.54 |
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| HG004 | 30039 | 11850 | 2.53 | 30027 | 11833 | 2.54 |
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| HG002 | 29955 | 11693 | 2.56 | 29942 | 11673 | 2.57 |
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| HG003 | 29852 | 11769 | 2.54 | 29842 | 11746 | 2.54 |
270+
| HG004 | 30048 | 11838 | 2.54 | 30037 | 11821 | 2.54 |
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If you want to restrict to the truth BED files, use this command:
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@@ -290,9 +290,9 @@ Which resulted in this table:
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| Sample | [3]ts | [4]tv | [5]ts/tv | [6]ts (1st | [7]tv (1st | [8]ts/tv (1st |
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: : : : : ALT) : ALT) : ALT) :
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| ------ | ----- | ----- | -------- | ---------- | ---------- | ------------- |
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| HG002 | 27704 | 10546 | 2.63 | 27696 | 10533 | 2.63 |
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| HG003 | 27356 | 10514 | 2.60 | 27351 | 10502 | 2.60 |
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| HG004 | 27491 | 10604 | 2.59 | 27484 | 10593 | 2.59 |
293+
| HG002 | 27716 | 10549 | 2.63 | 27708 | 10536 | 2.63 |
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| HG003 | 27382 | 10527 | 2.60 | 27378 | 10515 | 2.60 |
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| HG004 | 27503 | 10607 | 2.59 | 27496 | 10596 | 2.59 |
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### Rtg vcfstats
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@@ -314,69 +314,69 @@ HG002:
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315315
```
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Location : /data/HG002.vcf.gz
317-
Failed Filters : 14598
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Passed Filters : 45258
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SNPs : 41584
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Failed Filters : 14566
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Passed Filters : 45290
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SNPs : 41615
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MNPs : 0
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Insertions : 1867
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Deletions : 1783
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Indels : 22
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Same as reference : 2
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SNP Transitions/Transversions: 2.56 (41838/16338)
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Total Het/Hom ratio : 1.49 (27087/18169)
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SNP Het/Hom ratio : 1.51 (25017/16567)
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Insertions : 1874
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Deletions : 1779
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Indels : 21
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Same as reference : 1
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SNP Transitions/Transversions: 2.56 (41843/16345)
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Total Het/Hom ratio : 1.49 (27130/18159)
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SNP Het/Hom ratio : 1.51 (25066/16549)
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MNP Het/Hom ratio : - (0/0)
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Insertion Het/Hom ratio : 1.08 (969/898)
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Deletion Het/Hom ratio : 1.53 (1079/704)
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Indel Het/Hom ratio : - (22/0)
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Insertion/Deletion ratio : 1.05 (1867/1783)
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Indel/SNP+MNP ratio : 0.09 (3672/41584)
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Insertion Het/Hom ratio : 1.07 (967/907)
330+
Deletion Het/Hom ratio : 1.53 (1076/703)
331+
Indel Het/Hom ratio : - (21/0)
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Insertion/Deletion ratio : 1.05 (1874/1779)
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Indel/SNP+MNP ratio : 0.09 (3674/41615)
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```
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HG003:
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338338
```
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Location : /data/HG003.vcf.gz
340-
Failed Filters : 15423
341-
Passed Filters : 45150
342-
SNPs : 41519
340+
Failed Filters : 15383
341+
Passed Filters : 45190
342+
SNPs : 41585
343343
MNPs : 0
344-
Insertions : 1851
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Deletions : 1752
346-
Indels : 21
347-
Same as reference : 7
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SNP Transitions/Transversions: 2.52 (41645/16537)
349-
Total Het/Hom ratio : 1.48 (26923/18220)
350-
SNP Het/Hom ratio : 1.50 (24879/16640)
344+
Insertions : 1843
345+
Deletions : 1743
346+
Indels : 18
347+
Same as reference : 1
348+
SNP Transitions/Transversions: 2.52 (41678/16558)
349+
Total Het/Hom ratio : 1.48 (26984/18205)
350+
SNP Het/Hom ratio : 1.50 (24960/16625)
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MNP Het/Hom ratio : - (0/0)
352-
Insertion Het/Hom ratio : 1.11 (974/877)
353-
Deletion Het/Hom ratio : 1.49 (1049/703)
354-
Indel Het/Hom ratio : - (21/0)
355-
Insertion/Deletion ratio : 1.06 (1851/1752)
356-
Indel/SNP+MNP ratio : 0.09 (3624/41519)
352+
Insertion Het/Hom ratio : 1.09 (962/881)
353+
Deletion Het/Hom ratio : 1.49 (1044/699)
354+
Indel Het/Hom ratio : - (18/0)
355+
Insertion/Deletion ratio : 1.06 (1843/1743)
356+
Indel/SNP+MNP ratio : 0.09 (3604/41585)
357357
```
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359359
HG004:
360360

361361
```
362362
Location : /data/HG004.vcf.gz
363-
Failed Filters : 15166
364-
Passed Filters : 45515
365-
SNPs : 41857
363+
Failed Filters : 15176
364+
Passed Filters : 45505
365+
SNPs : 41856
366366
MNPs : 0
367-
Insertions : 1859
368-
Deletions : 1778
369-
Indels : 20
367+
Insertions : 1860
368+
Deletions : 1766
369+
Indels : 22
370370
Same as reference : 1
371-
SNP Transitions/Transversions: 2.55 (41671/16373)
372-
Total Het/Hom ratio : 1.57 (27794/17720)
373-
SNP Het/Hom ratio : 1.59 (25691/16166)
371+
SNP Transitions/Transversions: 2.55 (41681/16348)
372+
Total Het/Hom ratio : 1.57 (27795/17709)
373+
SNP Het/Hom ratio : 1.59 (25703/16153)
374374
MNP Het/Hom ratio : - (0/0)
375-
Insertion Het/Hom ratio : 1.12 (983/876)
376-
Deletion Het/Hom ratio : 1.62 (1100/678)
377-
Indel Het/Hom ratio : - (20/0)
378-
Insertion/Deletion ratio : 1.05 (1859/1778)
379-
Indel/SNP+MNP ratio : 0.09 (3657/41857)
375+
Insertion Het/Hom ratio : 1.11 (980/880)
376+
Deletion Het/Hom ratio : 1.61 (1090/676)
377+
Indel Het/Hom ratio : - (22/0)
378+
Insertion/Deletion ratio : 1.05 (1860/1766)
379+
Indel/SNP+MNP ratio : 0.09 (3648/41856)
380380
```
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382382
### Run hap.py to calculate the accuracy of DeepVariant generated call sets
@@ -405,6 +405,6 @@ Accuracy F1 scores:
405405

406406
Sample | Indel | SNP
407407
------ | -------- | --------
408-
HG002 | 0.974074 | 0.993897
409-
HG003 | 0.972967 | 0.993939
410-
HG004 | 0.972967 | 0.993939
408+
HG002 | 0.974037 | 0.994146
409+
HG003 | 0.968448 | 0.993913
410+
HG004 | 0.972569 | 0.994189

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