calling deletions and duplications in the cancer genomes
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4.8 years ago
Bogdan ★ 1.1k

Dear all,

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
genome deletion duplication • 1.3k views

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