Entering edit mode
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
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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] Rsamtools2.0.0 Biostrings2.52.0 XVector0.24.0
[7] SummarizedExperiment1.14.0 DelayedArray0.10.0 BiocParallel1.18.0
[10] matrixStats0.54.0 customProDB1.24.0 biomaRt2.40.1
[13] GenomicFeatures1.36.3 AnnotationDbi1.46.0 Biobase2.44.0
[16] GenomicRanges1.36.0 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] bitops1.0-6 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] memoise1.1.0 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] grid3.6.0 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] crayon1.3.4
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