Entering edit mode
6.0 years ago
cy.tang
•
0
Hi all,
Bioinformatics newcomer here. I have a vcf file from transposon detection software Mobster that looks like this:
CHROM POS ID REF ALT QUAL FILTER
chr11 34288 . . <INS:ME:ALU> . PASS
chr11 43445 . . <INS:ME:L1> . PASS
chr11 67645 . . <INS:ME:SVA> . PASS
I want to annotate these transposon insertion points and I've used ANNOVAR hg19 refGene. However, all of these insertion points are being treated as invalid inputs. Is it because there is no ref and alt bases?. Can someone give me some guidance on other ways to annotate it?
Thanks
did you try to replace the missing reference allele with 'N' ?
I just did. but when I run the command:
it tells me this when its generating an input for annotate_variation.pl: