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improve handling of DeepVariant non-called records
Compared to other callers, DeepVariant generates more non-called (./.) gVCF records to express uncertainty; including both reference bands and variant records. In 497277a we made sure to preserve the non-called status for reference bands, albeit in a heavy-handed way that censored all the QC fields (RNC=PartialData). Here we introduce a new RNC InputNonCalled, used for both reference bands and variant records when applicable, which preserves the associated QC fields in the pVCF.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,95 @@ | ||
| readme: | | ||
| 1000G chr21_5583275_G_T | ||
| A site exercising corner behaviors with a low-quality allele, non-called reference bands, | ||
| and RefCall variant records. | ||
| input: | ||
| header : |- | ||
| ##fileformat=VCFv4.2 | ||
| ##FILTER=<ID=PASS,Description="All filters passed"> | ||
| ##FILTER=<ID=RefCall,Description="Genotyping model thinks this site is reference."> | ||
| ##FILTER=<ID=LowQual,Description="Confidence in this variant being real is below calling threshold." | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | ||
| ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth of all passing filters reads."> | ||
| ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block."> | ||
| ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele"> | ||
| ##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions."> | ||
| ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype likelihoods, log10 encoded"> | ||
| ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Genotype likelihoods, Phred encoded"> | ||
| ##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> | ||
| ##contig=<ID=chr21,length=48129895> | ||
| ##contig=<ID=chr22,length=51304566> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT | ||
| body: | ||
| - HG00096.gvcf: | | ||
| HG00096 | ||
| chr21 5583273 . G <*> 0 . END=5583274 GT:GQ:MIN_DP:PL 0/0:15:5:0,15,149 | ||
| chr21 5583275 . G T,<*> 1 RefCall . GT:GQ:DP:AD:VAF:PL ./.:7:5:2,3,0:0.6,0:0,12,7,990,990,990 | ||
| chr21 5583276 . T <*> 0 . END=5583283 GT:GQ:MIN_DP:PL 0/0:15:5:0,15,149 | ||
| - HG00097.gvcf: | | ||
| HG00097 | ||
| chr21 5583273 . G <*> 0 . END=5583274 GT:GQ:MIN_DP:PL 0/0:9:3:0,9,89 | ||
| chr21 5583275 . G <*> 0 . END=5583275 GT:GQ:MIN_DP:PL ./.:0:3:20,0,50 | ||
| chr21 5583276 . T <*> 0 . END=5583280 GT:GQ:MIN_DP:PL 0/0:9:3:0,9,89 | ||
| - HG00099.gvcf: | | ||
| HG00099 | ||
| chr21 5583256 . G <*> 0 . END=5583274 GT:GQ:MIN_DP:PL 0/0:18:6:0,18,179 | ||
| chr21 5583275 . G T,<*> 0.5 RefCall . GT:GQ:DP:AD:VAF:PL ./.:10:6:3,3,0:0.5,0:0,9,21,990,990,990 | ||
| chr21 5583276 . T <*> 0 . END=5583290 GT:GQ:MIN_DP:PL 0/0:18:6:0,18,179 | ||
| - HG01377.gvcf: | | ||
| HG01377 | ||
| chr21 5583188 . C <*> 0 . END=5583274 GT:GQ:MIN_DP:PL 0/0:6:2:0,9,89 | ||
| chr21 5583275 . G T,<*> 10.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:9:3:1,2,0:0.666667,0:10,11,0,990,990,990 | ||
| chr21 5583276 . T <*> 0 . END=5583277 GT:GQ:MIN_DP:PL 0/0:9:3:0,9,89 | ||
| config_preset: DeepVariant | ||
|
|
||
| unifier_config: | ||
| min_AQ1: 10 | ||
| min_AQ2: 10 | ||
| min_GQ: 10 | ||
| monoallelic_sites_for_lost_alleles: true | ||
|
|
||
| truth_discovered_alleles: | ||
| - range: {ref: chr21, beg: 5583275, end: 5583275} | ||
| dna: 'G' | ||
| is_ref: true | ||
| all_filtered: false | ||
| top_AQ: [0] | ||
| zygosity_by_GQ: [[0,0],[0,0],[0,0],[0,0],[0,0],[0,0],[0,0],[0,0],[0,0],[0,0]] | ||
| - range: {ref: chr21, beg: 5583275, end: 5583275} | ||
| dna: 'T' | ||
| is_ref: false | ||
| all_filtered: false | ||
| top_AQ: [10] | ||
| zygosity_by_GQ: [[0,1],[0,0],[0,0],[0,0],[0,0],[0,0],[0,0],[0,0],[0,0],[0,0]] | ||
|
|
||
| truth_unified_sites: | ||
| - range: {ref: chr21, beg: 5583275, end: 5583275} | ||
| alleles: | ||
| - dna: G | ||
| - dna: T | ||
| quality: 10 | ||
| frequency: 0.125 # unifier puts 1/2N floor under frequency as long as AQ is sufficient | ||
| quality: 10 | ||
|
|
||
| truth_output_vcf: | ||
| - truth.vcf: | | ||
| ##fileformat=VCFv4.2 | ||
| ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency estimate for each alternate allele"> | ||
| ##INFO=<ID=AQ,Number=A,Type=Integer,Description="Allele Quality score reflecting evidence from all samples (Phred scale)"> | ||
| ##FILTER=<ID=PASS,Description="All filters passed"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | ||
| ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Genotype likelihoods, Phred encoded"> | ||
| ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> | ||
| ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> | ||
| ##FORMAT=<ID=RNC,Number=G,Type=Character,Description="Reason for No Call in GT: . = n/a, M = Missing data, P = Partial data, D = insufficient Depth of coverage, - = unrepresentable overlapping deletion, L = Lost/unrepresentable allele (other than deletion), U = multiple Unphased variants present, O = multiple Overlapping variants present"> | ||
| ##contig=<ID=21,length=48129895> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 HG00099 HG01377 | ||
| chr21 5583275 chr21_5583275_G_T G T 10 . AF=0.125;AQ=10 GT:DP:AD:GQ:PL:RNC ./.:5:2,3:7:0,12,7:II ./.:3:3,0:0:.:II ./.:6:3,3:10:0,9,21:II 1/1:3:1,2:1:10,11,0:.. |
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