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| # Created by .ignore support plugin (hsz.mobi) | ||
| # PyCharm | ||
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| # Cascadia v0.6 Release Notes (June 2018) | ||
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| # Table of Contents | ||
| - [Overview](#Overview) | ||
| - [Dataset Summary](#v06-truthset) | ||
| - [Validation Scheme](#validation-scheme) | ||
| - [Merging and Refining Scheme](#merging-and-refining-scheme) | ||
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| ## Overview | ||
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| A **hg38** truth set of simple deletion and insertions built from: | ||
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| - Manta deletion and insertion calls from NovaSeq NA12877 & NA12878 (NSV4 pipeline on hg38) | ||
| - This part of is the same as in v0.5 (except for minor VCF format fix) | ||
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| - Refined Sniffles (v1.0.8) deletion and insertion calls from PacBio NA12878 on hg38 | ||
| - Insertion sequence was assembled and refined from PacBio + ONT reads | ||
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| - copy number variants and large deletions curated from population and Platinum Genome pedigree on *hg19*, coming from deletion calls of Manta/Canvas and Sniffles. | ||
| - Please see Xiao's CNV truth set repository for details: | ||
| - https://git.illumina.com/xchen2/CNVTruthSet | ||
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| Hg19 truth set is generated by lift-over on hg38 truth set. | ||
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| 12,374 (98%) passed entries and 24,405 (88%) failed entries were successfully converted to hg19. | ||
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| The release vcf contains genotypes of NA12877 and NA12878 (re-genotyped with our targeted graph genotyper *Paragraph*). | ||
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| Illumina cluster users can find VCF containing full Platinum Genome pedigree genotypes on Illumina cluster. | ||
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| ### Unvalidated variants | ||
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| In addition, VCFs named with "all_merge.include_unvalidated" contain unvalidated variants from Sniffles v1.0.8 calls, they are: | ||
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| - All calls on chrX, chrY and mitochondria | ||
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| - Inversions, duplications and translocations | ||
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| These unvalidated variants are labled as *UNVALIDATED* in their filter fields. | ||
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| For now we haven't established a robust pipeine for validating these variants, but finally they will be validated in future release. | ||
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| ### Data format | ||
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| Variants that pass our pedigree and population check were labeled as *PASS* in their filter fields. | ||
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| Variants that fail any filter were labled with the specific filter name(s) in their filter fields. | ||
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| *SOURCE* key in *INFO* field indicates where the variant originally comes from. All unvalidated variants do not have *SOURCE* key because they all come from Sniffles. | ||
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| ## Dataset Summary | ||
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| ### Merged variants partitioned by SVLEN and type | ||
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| | SV Type | INS | INS | DEL | DEL | CNV | CNV | | ||
| |:----------------------|:---------:|:---------:|:---------:|:---------:|:---------:|:---------:| | ||
| | Filter | PASS | FAIL | PASS | FAIL | PASS | FAIL | | ||
| | _L_ \< 50 | 905 | 1,934 | 1,178 | 1,390 | 0 | 0 | | ||
| | 50 \< _L_ \< 100 bp | 1,503 | 3,571 | 1,939 | 3,553 | 0 | 0 | | ||
| | 100 \< _L_ \< 1kb | 2,240 | 4,785 | 2,389 | 4,417 | 0 | 0 | | ||
| | 1kb \< _L_ \< 10kb | 18 | 155 | 1,978 | 2,930 | 105 | 139 | | ||
| | _L_ > 10kb | 0 | 0 | 337 | 1,065 | 89 | 219 | | ||
| | __Total__ | __4,666__ | __10,445__| __7,821__ | __13,355__| __194__ | __358__ | | ||
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| ### **Non-reference** calls in NA12878 partitioned by SVLEN and type | ||
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| | SV Type | INS | DEL | CNV | | ||
| |:----------------------|:---------:|:---------:|:---------:| | ||
| | _L_ \< 50 | 878 | 1,169 | 0 | | ||
| | 50 \< _L_ \< 100 bp | 1,274 | 1,521 | 0 | | ||
| | 100 \< _L_ \< 1kb | 1,958 | 1,926 | 0 | | ||
| | 1kb \< _L_ \< 10kb | 17 | 626 | 19 | | ||
| | _L_ > 10kb | 0 | 140 | 11 | | ||
| | __Total__ | __4,127__ | __5,382__ | __30__ | | ||
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| ### Merged variants partitioned by SVLEN, type and source | ||
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| | SV Type | INS | INS | DEL | DEL | | ||
| |:----------------------|:--------------|:--------------|:--------------|:--------------| | ||
| | Source | Manta PASS | Sniffles PASS | Manta PASS | Sniffles PASS | | ||
| | _L_ \< 50 | 6 (24%) | 901 (32%) | 7 (100%) | 1,178 (46%) | | ||
| | 50 \< _L_ \< 100 bp | 1,151 (47%) | 620 (22%) | 1,598 (44%) | 726 (32%) | | ||
| | 100 \< _L_ \< 1kb | 1,451 (55%) | 1,189 (25%) | 2,256 (45%) | 1,492 (47%) | | ||
| | 1kb \< _L_ \< 10kb | 1 (100%) | 18 (10%) | 736 (29%) | 267 (66%) | | ||
| | _L_ > 10kb | 0 (n/a) | 0 (n/a) | 156 (17%) | 0 (n/a) | | ||
| | __Total__ |__2,606 (51%)__|__2,728 (26%)__|__4,753 (39%)__|__3,663 (43%)__| | ||
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| Using refined Sniffles calls as input, v0.6 has a significant improved validate rate for Sniffles calls, with 2,604 validated insertions and a validation rate of 26%, compared to v0.5 (589 validated insertions and a validation rate of 5%). | ||
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| ## Merging Scheme | ||
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| For simple SVs validated by Paragraph, we followed the same merging scheme for deletions as [v0.5](../v0.5/README.md). | ||
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| For CNVs, we do not try to merge them with simple SVs. | ||
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| For large deletions labeled as PASS, we prioritize Paragraph validated ones over Xiao's CNV truth set. |