<p><em>Answer from @Kozolovska, converted from comment:</em></p>
<p>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.</p>

CC BY-SA 4.0
2021-07-04T04:27:14.133Z
2021-07-04T04:27:14.133Z
gringer
<p>I have a problem with using <code>rbind</code> to combine VCF files using the library <a href="https://bioconductor.org/packages/VariantAnnotation" rel="nofollow noreferrer">VariantAnnotation</a> from Bioconductor.</p>
<p>I am reading two VCF files, when I try to combine them in a certain order with <code>rbind</code> I'm getting an error. When I combine them in a different order, it works fine.</p>
<pre><code>vcf.full &lt;- rbind(vcf1, vcf2) ## Doesnt work 
</code></pre>
<blockquote>
<p>Error in as(from, to_class, strict = FALSE) :    no method or default
for coercing “CompressedCharacterList” to “DNAStringSetList”</p>
</blockquote>
<pre><code>vcf.full &lt;- 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
</code></pre>
<p>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?</p>

<r><vcf>
Combine VCF files
# Combine VCF files

(Asked by: username_0 on 2018-08-16)

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?

**Tags:** r, vcf

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## 1 answers

### Answer by username_1 on 2021-07-04. Score: 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.


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