[chr5:36023180-39360025][DUP][SVLEN=3336845bp]

[jzook]

chr5 36023180 Minda_112 N <DUP> . PASS SVLEN=3336845;SVTYPE=DUP;SUPP_VEC=PB_severus_BND5690_2,PB_r_284,ONT_severus_DUP6554,ONT_r_183,ILL_MantaDUP:TANDEM:97365:0:1:0:0:0,ILL_2945609644:2,ILL_gridss91bf_9914h,PB_ID_11898_2,PB_Sniffles2.DUP.18CM4,ONT_ID_30383_2,ONT_Sniffles2.DUP.192M4

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr5:36023180#ribbon

[nate-d-olson]

Ribbon and SplitThreader show support for SV. ONT and PacBio CCS support SV no change in coverage for Element supporting the SV call but supported by mate pairs.

• No similar variants within a few kb. The variant is within a 135Mb INV in the DRAGEN SV callset (variant info below).

• Breakpoints appear correct (IGV)

• It does not appear to be clonal, but it might just be a poorly phased region.

DRAGEN Inversion

ID: DRAGEN:INV:212597:0:1:0:0:0
Chr: chr5
Position: 20,023,769-155,777,978
Reference: C*
Alternate:  
Qual: .
Type: SYMBOLIC
Is Filtered Out: No
Alleles:
Alternate Alleles:  
Variant Attributes
INV3: true
HOMSEQ: CA
JUNCTION_SOMATICSCORE: 585
SOMATICSCORE: 1165
CIEND: [-2, 0]
SVLEN: 135754209
EVENT: DRAGEN:INV:212597:0:1:0:0:0
SOMATIC: true
HOMLEN: 2
SVTYPE: INV
END: 155777978
CIPOS: [0, 2]

[jzook]

This looks likely clonal to me since the cov increases from ~200 to 300 and ~1/3 HiFi reads support the duplication