please could you help with the interpretation of the following finding: I have being using several SV callers (including MANTA) to call structural variants in the cancer genomes. In one case, the prediction is of a deletion overlapping almost completed an area that is duplicated (please see below the coordinates), and the question is : in the absence of SNV information, is it possible to call deletion on a chromosome and duplication on the other chromosome ? Or possibly, is there any other interpretation ? thank you ;) !
chr6 90862603 90862605 chr6 154131276 154131278** *MantaDUP:TANDEM:89876:3:4:0:0:0* DUP PASS END=154131277;SVTYPE=DUP;SVLEN=63268673;CIPOS=0,1;CIEND=0,1;HOMLEN=1;HOMSEQ=G;SOMATIC;SOMATICSCORE=159 PR:SR 52,0:61,0 52,41:55,21 chr6 90869227 90869228 chr6 157151560 157151561** *MantaDEL:89876:1:2:0:1:0* DEL PASS END=157151561;SVTYPE=DEL;SVLEN=-66282333;SVINSLEN=5;SVINSSEQ=TTGCC;SOMATIC;SOMATICSCORE=108 PR:SR 40,0:45,0 39,23:47,22