Missing END2 in Gnomad SVs VCF

Structural Variation
1

Hello!

I’m using the public gnomad sites VCF as input to another tool (gatk SVConcordance) and received an error about missing END2 in the VCF:

Bad input: Attributes END2 and CHR2 are required for BND and CTX records

It appears as though END2 isn’t present as an info annotations when CHR2 is equal to CHR1 and the END is equal to the start coordinate. Is that the correct assumption?

2

Thanks for your question!

You’re correct that BND records where CHR2 is equal to CHROM may not have the END2 field in INFO in the gnomAD SV VCF. GATK-SV’s behavior has changed since the gnomAD VCF was produced, and GATK SVConcordance expects the newer behavior in which all BNDs have END2.

Here are a couple of options to work around this mismatch:

  1. Set END2 = POS+SVLEN for BNDs missing END2
  2. Exclude BNDs from the VCF prior to running GATK SVConcordance if they are not of interest to you

We expect that this issue only applies to BNDs, but if you observe missing END2 fields for CTX records as well, please let us know.

I hope this helps!

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