VEP annotation of Manta BND

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5.0 years ago

lindak • 0

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?

Annnotation VEP • 4.5k views

ADD COMMENT • link updated 5.0 years ago by Emily 23k • written 5.0 years ago by lindak • 0

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

ADD REPLY • link 5.0 years ago by Pierre Lindenbaum 161k

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What format are your translocations inputted in?

ADD REPLY • link 5.0 years ago by Emily 23k

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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 REPLY • link 5.0 years ago by lindak • 0

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

ADD REPLY • link 5.0 years ago by Pierre Lindenbaum 161k

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Yes, I can see that.

ADD REPLY • link 5.0 years ago by Emily 23k

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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...