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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
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SURVIVOR not reporting DR #146

Open Akazhiel opened 3 years ago

Akazhiel commented 3 years ago

Hello!

Upon using SURVIVOR to merge 2 VCF files from the same caller, I've noticed that the DR field always report 0,0 despite the reads information being available in both the VCF files. What could be the reason of this?

Best regards, Jonatan

fritzsedlazeck commented 3 years ago

Which SV caller are you using ? VCF files are always different between callers and that makes it sometimes hard to parse this field correctly

Akazhiel commented 3 years ago

I am using different variant callers since I'm trying to call for somatic mutations and thus I need to verify the variants are called in different callers. For this exact issue I was just merging 2 VCF from the same caller, one for Normal and one for Tumor. The variant caller used was SVIM.

johannesgeibel commented 2 years ago

Hi, I actually also run into the same problem merging sniffles vcf output files with the latest commit of SURVIVOR. The DR field is correctly copied into the position for the reference allele in the new vcf, while the info of the DV field is removed. A fix for some common callers would be a nice enhancement.