CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
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Elena.M • 0
@elenam-21324
Last seen 3.4 years ago
Switzerland

Hello,

I am trying to use the package CustomProDB to retrieve the mutated peptides from a VCF file. When I use InputVcf(), the GRanges object does not include the INDEL column that I need for making the index and use Varlocation(). I have generated the VCF file using GATK HaplotypeCaller. Any idea why?

Thank you very much in advance, E.

> vcf <- InputVcf("/Users/elena/Desktop/Paulino/4T07_DNA.vcf")
Warning message:
In rbind(...) :
  number of columns of result is not a multiple of vector length (arg 1)
> length(vcf)
[1] 1
> table(values(vcf[[1]])[['INDEL']])
< table of extent 0 >
> vcf[[1]][1:3]
GRanges object with 3 ranges and 32 metadata columns:
                seqnames    ranges strand |         REF         ALT      QUAL      FILTER     AC     AF        AN BaseQRankSum        DP
                   <Rle> <IRanges>  <Rle> | <character> <character> <numeric> <character> <list> <list> <integer>    <numeric> <integer>
  1:3026194_C/A        1   3026194      * |           C           A     72.28           .      2      1         2         <NA>         2
  1:3053912_G/T        1   3053912      * |           G           T     111.8           .      2      1         2         <NA>         3
  1:3070694_C/A        1   3070694      * |           C           A      55.6           .      1    0.5         2            0         6
                       DS ExcessHet        FS InbreedingCoeff  MLEAC  MLEAF        MQ MQRankSum        QD ReadPosRankSum       SOR          GT
                <logical> <numeric> <numeric>       <numeric> <list> <list> <numeric> <numeric> <numeric>      <numeric> <numeric> <character>
  1:3026194_C/A     FALSE    3.0103         0            <NA>      1    0.5        60      <NA>     25.36           <NA>     2.303         1/1
  1:3053912_G/T     FALSE    3.0103         0            <NA>      1    0.5        60      <NA>     28.73           <NA>     2.833         1/1
  1:3070694_C/A     FALSE    3.0103         0            <NA>      1    0.5      49.2    -0.842      9.27          1.834     0.307         0/1
                         AD        AD.1        AD.2        DP.1          GQ          PL        PL.1        PL.2        PL.3        PL.4
                <character> <character> <character> <character> <character> <character> <character> <character> <character> <character>
  1:3026194_C/A           0           2           0           2           6          84           6           0          84           6
  1:3053912_G/T           0           3           0           3           9         125           9           0         125           9
  1:3070694_C/A           4           2           4           6          63          63           0         149          63           0
                       PL.5
                <character>
  1:3026194_C/A           0
  1:3053912_G/T           0
  1:3070694_C/A         149
  -------
  seqinfo: 22 sequences from an unspecified genome; no seqlengths
vcf snv gatk customprodb inputvcf • 397 views
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sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding

locale: [1] C

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] rtracklayer1.44.0 TxDb.Mmusculus.UCSC.mm10.knownGene3.4.7 VariantAnnotation1.30.1
[4] Rsamtools
2.0.0 Biostrings2.52.0 XVector0.24.0
[7] SummarizedExperiment1.14.0 DelayedArray0.10.0 BiocParallel1.18.0
[10] matrixStats
0.54.0 customProDB1.24.0 biomaRt2.40.1
[13] GenomicFeatures1.36.3 AnnotationDbi1.46.0 Biobase2.44.0
[16] GenomicRanges
1.36.0 GenomeInfoDb1.20.0 IRanges2.18.1
[19] S4Vectors0.22.0 BiocGenerics0.30.0

loaded via a namespace (and not attached): [1] Rcpp1.0.1 BiocManager1.30.4 plyr1.8.4 compiler3.6.0 prettyunits1.0.2
[6] bitops
1.0-6 tools3.6.0 progress1.2.2 zlibbioc1.30.0 digest0.6.20
[11] bit1.1-14 AhoCorasickTrie0.1.0 BSgenome1.52.0 lattice0.20-38 RSQLite2.1.1
[16] memoise
1.1.0 pkgconfig2.0.2 rlang0.4.0 Matrix1.2-17 DBI1.0.0
[21] curl3.3 GenomeInfoDbData1.2.1 stringr1.4.0 httr1.4.0 hms0.4.2
[26] grid
3.6.0 bit640.9-7 R62.4.0 XML3.98-1.20 blob1.1.1
[31] magrittr1.5 GenomicAlignments1.20.1 assertthat0.2.1 stringi1.4.3 RCurl1.95-4.12
[36] crayon
1.3.4
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