Why Some REPTYPE=CONTRAC Records Have Longer ALT Length than REF Length

[yueyaog]

Hi @nhansen,

I am going through a SVWIDEN output of HG002 VCF. I have noticed that there are some variants that were annotated REPTYPE=CONTRAC has longer ALT than REF. I expect CONTRAC records should have shorter ALT length than REF length because CONTRAC is a type of DEL. I have attached an instance below.

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	syndip
chr1	1108885	.	G	GTCCACCACAGCCACCATGTCTCGGCAGCACCGTCCACCACAGCCACCATGTCTCGGCAGCACCGTTCACCACAGCCACCATGTCTCAGCACCA	30	.	REPTYPE=CONTRAC;BREAKSIMLENGTH=7699;REFWIDENED=chr1:1108048-1115663	GT:AD	0|1:1,1

Do you have any explanations for this?

[nhansen]

Hi @yueyaog. That's clearly a bug--can you provide me the initial VCF entry and the reference it's aligned to?

[yueyaog]

Sure. I didn't generate this SVWIDEN output myself. I got a copy of it from Justin Zook from NIST. I will send you a separate email with details.