Matching Variants Between Two VCF Objects
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Dario Strbenac ★ 1.5k
@dario-strbenac-5916
Last seen 6 days ago
Australia

If I have two VCF objects, how can I find the matches of one in the other, considering both the location and the alternative allele? I used match, but I find that it only matches on position and ignores whether the alterative allele is different (row ranges not shown).

> fixedQuery
DataFrame with 1 row and 4 columns
             REF                    ALT      QUAL      FILTER
  <DNAStringSet>        <CharacterList> <numeric> <character>
1              T .AAAAAAAAAAAAAAAAAAA..   4115.21        PASS
> fixedMatch
DataFrame with 1 row and 4 columns
             REF                    ALT      QUAL      FILTER
  <DNAStringSet>        <CharacterList> <numeric> <character>
1              T .TTTCCCCTGATGAGTGTCT..   4824.64        PASS

It's possible to use ref and alt and match those too, but I thought there might be some higher-level solution.

VariantAnnotation • 674 views
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2
Entering edit mode
nick.eagles ▴ 100
@nickeagles-24264
Last seen 2.1 years ago

Hello,

Are you referring to 2 CollapsedVCF objects each with 1 column (sample)? I assume this is the case, since a CollapsedVCF containing more than one sample may have more than one allele for a particular position (potentially different alleles in each sample). I don't know of a high-level function for your use-case, so the best I can provide is a custom function that should do the job. The below function returns a CollapsedVCF whose rows are the sites from vcf1 whose ranges and genotype calls are present and equal as in vcf2.

getEqualOverlaps = function(vcf1, vcf2) {
    #  This function only makes sense for VCF files with one sample!
    stopifnot(ncol(vcf1) == 1 && ncol(vcf2) == 1)

    #  First take the ranges which are present in both VCF objects
    temp_vcf1 = subsetByOverlaps(vcf1, vcf2)

    #  The indices of each range in vcf2 along the rows of vcf1
    vcf2_indices = match(ranges(temp_vcf1), ranges(vcf2))

    #  Subset those equal ranges to those whose genotype calls match
    temp_vcf1 = temp_vcf1[geno(temp_vcf1)$GT[,1] == geno(vcf2)$GT[vcf2_indices,1],]

    return(temp_vcf1)
}

Best,

-Nick

P.S. I'm currently learn to help others.

Session info when testing this function:

> library('sessioninfo')
> session_info()
─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.0.3 Patched (2020-11-29 r79529)
 os       CentOS Linux 7 (Core)
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       US/Eastern
 date     2020-12-02

─ Packages ───────────────────────────────────────────────────────────────────
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 XVector              * 0.30.0   2020-10-27 [2] Bioconductor
 zlibbioc               1.36.0   2020-10-27 [2] Bioconductor

[1] /users/neagles/R/4.0.x
[2] /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0.x/R/4.0.x/lib64/R/site-library
[3] /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0.x/R/4.0.x/lib64/R/library
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