Question: calling deletions and duplications in the cancer genomes
0
gravatar for Bogdan
2.0 years ago by
Bogdan690
Palo Alto, CA, USA
Bogdan690 wrote:

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
duplication deletion genome • 706 views
ADD COMMENTlink modified 2.0 years ago by WouterDeCoster36k • written 2.0 years ago by Bogdan690
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1170 users visited in the last hour