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CNV benchmarking: Truvari & HG002 SVs v0.6 (GIAB)

Hi,

I ran truvari using the "HG002_SVs_Tier1_v0.6.vcf.gz" (both as true and query), with "HG002_SVs_Tier1_v0.6.bed", and everything is working.

Looking the HG002_SVs_Tier1_v0.6.vcf.gz vcf has the bellow format

#CHROM  POS     ID      REF     ALT

1   15785403   someID  TAAAAAAAAAAAAAAAAAAAA   T

My query format is like

1    15785403        someID:LOSS:1:15785403-15785423  N       DEL

Is there any tool to convert my query format in something like the v0.6 format?

Thanks

benchmarking truvari cnv
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updated by DBScan • DBScan • written by emma.a • emma.a

With which tool did you get your query format? To me this doesn't look like a valid VCF, but I may be wrong here.

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written by DBScan • DBScan

Hi, Illumina Basespace DRAGEN, but I also have another pipeline that the format of "REF" and "ALT" is the same as in my query vcf. I do not remember if also DRAGEN-GATK gives the same format (I do not have an example in my hands now).

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written by emma.a • emma.a

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