Comments (5)
I would need to see more context but something could be happening is that this run with --pick single
. The --pick
parameter controls how many matches a call is allowed to participate in (details).
Are there other calls in this region which were marked as true positive? If so consider using --pick multi
Otherwise I'm not sure. The base vcf entry you've provided shows the call was annotated:
PctSizeSimilarity=1;PctRecOverlap=0.9565;SizeDiff=0;StartDistance=-68;EndDistance=-68;GTMatch=0;TruScore=65;MatchId=94.0.0
So you could look through the tp-comp/fp VCFs for MatchId=94.0.*
To see what it was compared to. (MatchId details)
Also, If you turn on --debug
the logging is pretty verbose about exactly why any match decision is made.
If you're still stuck, if you could send me the input base/comp VCFs in the region, say chr12: 71959796-71965796
, I could help investigate it.
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Thank you @ACEnglish! I'll start with your suggestions and I'll let you know about the outcomes.
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Here it is the matched variant in the fp.vcf.gz, that is actually the one I was expecting to match:
chr12 71962796 DRAGEN:LOSS:chr12:71962797-71964360 N <DEL> 150 PASS SVLEN=-1564;SVTYPE=CNV;END=71964360;REFLEN=1564;OrigCnvPos=71962186;OrigCnvEnd=71964742;SVCLAIM=DJ;MatchSv=DRAGEN:DEL:183383:0:1:0:0:0;PctSeqSimilarity=0;PctSizeSimilarity=1;PctRecOverlap=0.9565;SizeDiff=0;StartDistance=-68;EndDistance=-68;GTMatch=0;TruScore=65;MatchId=94.0.0 GT:SM:CN:BC:GC:CT:AC:PE 1/1:0.263257:1:2:0.375978:0.507825:0.483959:39,42
They are also annotated with a high Overlapping score (PctRecOverlap=0.9565) so I do not see a reason to exclude them. Moreover, in the region there in no other variant, so I presume the --pick multiple won't help.
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Ah! I see what's happening, now. So there's another 'threshold' that wasn't accounted for typeignore
. It is off (false) by default. These variants don't have matching types, so they're not passing the thresholds.
Now, you and I can see that they do have matching types (DEL), but if you look at how truvari determines svtype you'll also see that the SVTYPE=CNV
in the comp vcf doesn't match the SVTYPE=DEL
in the base.
I know that vcf v4.4 had a lot of changes recently and in it SVTYPE was deprecated in favor of symbolic alts. This was not my favorite move because it's obviously a breaking change.
Regardless, the quickest way to get these variants to match is for you to run bcftools annotate -x INFO/SVTYPE
on the comp vcf.
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Ok, great, thanks for the help!!
Now it makes sense!
Have a nice day,
Valentina
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Related Issues (20)
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