Question: VEP annotation of Manta BND
0
gravatar for lindak
10 months ago by
lindak0
lindak0 wrote:

I am using VEP to annotate SVs from Manta vcf files. For the translocations (MantaBND) only the first reported chr region gets a gene annoation. Is there a way to get gene annotations for both chromosomes involved in the translocation?

vep annnotation • 609 views
ADD COMMENTlink modified 10 months ago by Emily_Ensembl20k • written 10 months ago by lindak0

duplicate the variant to create another one with the 2nd position.

ADD REPLYlink written 10 months ago by Pierre Lindenbaum126k

What format are your translocations inputted in?

ADD REPLYlink written 10 months ago by Emily_Ensembl20k

The structure of the VCF is:

chr1 84799235 MantaBND:6124:1:2:0:0:0:0 A A]chr14:85914438] . PASS SVTYPE=BND;MATEID=MantaBND:6124:1:2:0:0:0:1;IMPRECISE;CIPOS=-92,92;SOMATIC;SOMATICSCORE=34;BND_DEPTH=27;MATE_BND_DEPTH=31 PR

ADD REPLYlink modified 10 months ago • written 10 months ago by lindak0

@Emily_Ensembl the breakpoint is defined in the ALT column. A]chr14:85914438]

ADD REPLYlink written 10 months ago by Pierre Lindenbaum126k

Yes, I can see that.

ADD REPLYlink written 10 months ago by Emily_Ensembl20k

Sorry, I see now that Manta actually reports breakend translocations on double rows so 'chr14 85914438' comes further down a second row, which means that it gets a gene annotatation by VEP. Sorry, my bad...

ADD REPLYlink written 10 months ago by lindak0

no problem, please, close your question.

ADD REPLYlink written 10 months ago by Pierre Lindenbaum126k
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