Question: CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
0
gravatar for Elena.M
4 days ago by
Elena.M0
Switzerland
Elena.M0 wrote:

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
ADD COMMENTlink modified 4 days ago • written 4 days ago by Elena.M0

´´´

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
´´´

ADD REPLYlink modified 4 days ago • written 4 days ago by Elena.M0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 292 users visited in the last hour