Missing somatic translocation/insertion SV breakpoint

[aganezov]

Version: Severus 0.1.2
Data:

• Tumor: colo829
• Normal: colo829bl

command executed:

Severus-0.1.2/severus.py -t 16 --target-bam colo829.b2.bam --control-bam colo829bl.b2.bam --out-dir severus_unhaplotagged --vaf-thr 0.001 --single-bp

and

Severus-0.1.2/severus.py -t 16 --target-bam colo829.b2.tagged.bam --control-bam colo829bl.b2.tagged.bam --out-dir severus_haplotagged --vaf-thr 0.001 --single-bp 

The underlying situation is rather complex with a somatic trnalocation/insetion/foldback happening (see attached jbrowse2 view).

Severus output suggests no somatic SV presence on the left boundary. In the IGV screenshot below the supplementary alignment for a DUP-like even in HP2 is clearly visible. But does suggest presence of non-somatic translocation/SV.

For the right boundary, somatic translocation-like SV is reported by Severus.

Issue persists with both unhaplotagged and haplotagged input data.