13kb false duplication at chr10_MATERNAL:43,216,000-43,245,000

[nhansen]

Have you confirmed that this issue hasn't already been reported?

• I have confirmed in the UCSC browser hub that this is a new issue (required)

Issue location in assembly (use format chromosome:start-end, e.g., chr13_MATERNAL:3740148-9625296)

chr10_MATERNAL:43,216,000-43,245,000

Description of the issue

Sniffles calls on v0.9 picked up a large deletion in this region, and long read data bear it out. Here's an IGV screenshot:

[jzook]

I just came across this when looking at DV calls in both HiFi and ONT as well, and looks like it is annotated as a segdup between HSats in the browser. Some HG2 and HG4 HiFi reads align across it so should be possible to correct based on HiFi sequence as well as ONT

[jzook]

One thing I just noticed when looking at NateD's stratifications is that the 11kb region chr10_MATERNAL 43232301 43243056 is a pure C homopolymer! This made chr10 a huge outlier for long C homopolymers :)

[nhansen]

Wow--tagging @skoren so he can possibly figure out where all those C's came from! Just to be picky, though, it's not pure C's for the whole 11kb. There are actually non-C bases at about seven spots, giving eight very long mononucleotide runs!

[nhansen]

As you point out, Justin, it should be fairly easy to re-call consensus for this stretch to create a patch.

[jzook]

ah, I forgot that we merged nearby perfect homopolymers to get this region, so that makes sense that there could be small (<10bp) interruptions between 21+bp perfect homopolymers