Annotate transposon VCF file

Question

[cy.tang]

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

[Pierre Lindenbaum]

did you try to replace the missing reference allele with 'N' ?

 awk -F '\t' '{OFS="\t";if($4==".") $4="N";print}'  in.vcf > out.vcf

[cy.tang]

I just did. but when I run the command:

table_annovar.pl in.vcf humandb/ -buildver hg19 -out chr11 -remove -protocol refGene -operation g -vcfinput

it tells me this when its generating an input for annotate_variation.pl:

NOTICE: Running with system command <convert2annovar.pl -includeinfo -allsample -withfreq -format vcf4 in.vcf > chr11.avinput>
NOTICE: Finished reading 61 lines from VCF file
NOTICE: A total of 46 locus in VCF file passed QC threshold, representing 0 SNPs (0 transitions and 0 transversions) and 0 indels/substitutions
NOTICE: Finished writing allele frequencies based on 0 SNP genotypes (0 transitions and 0 transversions) and 0 indels/substitutions for 0 samples
WARNING: 46 invalid reference alleles found in input file

Answer 1

[WouterDeCoster]

vcfanno can handle these. I just tested it by changing ref and alt to '.' in a vcf file and annotate using a bed file.

[cy.tang]

Thank you I will give it a try!