Combine VCF files

Question

I have a problem with using rbind to combine VCF files using the library VariantAnnotation from Bioconductor.

I am reading two VCF files, when I try to combine them in a certain order with rbind I'm getting an error. When I combine them in a different order, it works fine.

vcf.full <- rbind(vcf1, vcf2) ## Doesnt work 

Error in as(from, to_class, strict = FALSE) : no method or default for coercing “CompressedCharacterList” to “DNAStringSetList”

vcf.full <- rbind(vcf2, vcf1) ## Work 

header(vcf1)
class: VCFHeader 
samples(503): NA06984 NA06989 ... NA20828 NA20832
meta(2): META contig
fixed(2): FILTER ALT
info(27): CIEND CIPOS ... EX_TARGET MULTI_ALLELIC
geno(1): GT

header(vcf2)
class: VCFHeader 
samples(503): NA06984 NA06989 ... NA20828 NA20832
meta(2): META contig
fixed(2): FILTER ALT
info(27): CIEND CIPOS ... EX_TARGET MULTI_ALLELIC
geno(1): GT

dim(vcf1)
[1]  30 503

dim(vcf2)
[1] 149 503

The two VCF files seem identical. Any idea of why it happens? Or any suggestions on a different method to combine multiple VCF files using R?

Answer 1

Answer from @Kozolovska, converted from comment:

Found the problem, some of ALT were structural variant, so the list of vcf2@info$ALT was a charterer list and not a 'DNAStringSetList' after removing that variant it worked. Thanks.