"Incompatible genome" error when using locateVariants

Question

[dktarathym]

I am having a vcf file :

> seqlevels(D784G)

[1] "chrI"    "chrII"   "chrIII"  "chrIV"   "chrIX"   "chrM"    "chrV"    "chrVI"   "chrVII"  "chrVIII"
[11] "chrX"    "chrXI"   "chrXII"  "chrXIII" "chrXIV"  "chrXV"   "chrXVI" 

> seqlevels(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene)

[1] "chrI"    "chrII"   "chrIII"  "chrIV"   "chrV"    "chrVI"   "chrVII"  "chrVIII" "chrIX"   "chrX"   
[11] "chrXI"   "chrXII"  "chrXIII" "chrXIV"  "chrXV"   "chrXVI"  "chrM"   

> loc <- locateVariants(D784G, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, AllVariants())

Error in mergeNamedAtomicVectors(genome(x), genome(y), what = c("sequence",  : 
  sequences chrI, chrII, chrIII, chrIV, chrIX, chrM, chrV, chrVI, chrVII, chrVIII, chrX, chrXI, chrXII, chrXIII, chrXIV, chrXV, chrXVI have incompatible genomes:
  - in 'x': TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene
  - in 'y': sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, sacCer3, 

How to handle it?

Do I need to re arrange the seqlevels of my vcf file? If yes, then how?

Sincerely,
Deepak

[dktarathym]

intersect(seqlevels(D784G),seqlevels(txdb))
 [1] "chrI"    "chrII"   "chrIII"  "chrIV"   "chrIX"   "chrM"    "chrV"    "chrVI"   "chrVII"  "chrVIII"
[11] "chrX"    "chrXI"   "chrXII"  "chrXIII" "chrXIV"  "chrXV"   "chrXVI" 

Answer 1

[Devon Ryan]

Have you tried changing the genome with genome(D784G) <- "sacCer3"? That might solve the problem.

[dktarathym]

Hi Devon,

Thank you so much.

It seems to work. Also, there are some warnings:

> genome(D784G) <- "sacCer3"
> loc <- locateVariants(D784G, txdb, AllVariants())
Warning messages:
1: In `start<-`(`*tmp*`, value = c(-1665L, -1462L, 480L, 8091L, 10046L,  :
  trimmed start values to be positive
2: In `end<-`(`*tmp*`, value = c(534L, 737L, 2679L, 10290L, 12245L,  :
  trimmed end values to be <= seqlengths
3: In `start<-`(`*tmp*`, value = c(-981575L, -802723L, -802656L, -802572L,  :
  trimmed start values to be positive
4: In `end<-`(`*tmp*`, value = c(1018425L, 1197277L, 1197344L, 1197428L,  :
  trimmed end values to be <= seqlengths
> loc
GRanges with 9269 ranges and 7 metadata columns:
                 seqnames           ranges strand   |   LOCATION   QUERYID      TXID
                    <Rle>        <IRanges>  <Rle>   |   <factor> <integer> <integer>
  chrI:18425_T/C     chrI [ 18425,  18425]      *   | intergenic         1      <NA>
                     chrI [ 25479,  25479]      -   |     coding         2        66
                     chrI [141030, 141030]      +   |     coding         3        38
                     chrI [141030, 141030]      +   |   promoter         3        39
                     chrI [141030, 141030]      -   |     coding         3       103
             ...      ...              ...    ... ...        ...       ...       ...
                   chrXVI [869062, 869062]      -   |   promoter      4301      6644
                   chrXVI [869062, 869062]      -   |     coding      4301      6645
                   chrXVI [890346, 890346]      +   |     coding      4302      6395
                   chrXVI [890346, 890346]      +   |   promoter      4302      6396
                   chrXVI [890346, 890346]      -   |   promoter      4302      6650
                     CDSID      GENEID                   PRECEDEID
                 <integer> <character>             <CharacterList>
  chrI:18425_T/C      <NA>        <NA> YAL001C,YAL002W,YAL003W,...
                        68     YAL063C                            
                        39     YAL004W                            
                      <NA>     YAL003W                            
                       105     YAL005C                            
             ...       ...         ...                         ...
                      <NA>     YPR162C                            
                      6972     YPR163C                            
                      6709     YPR175W                            
                      <NA>     YPR178W                            
                      <NA>     YPR174C                            
                                        FOLLOWID
                                 <CharacterList>
  chrI:18425_T/C YAL064C-A,YAL064W-B,YAL065C,...




             ...                             ...





  ---
  seqlengths:
      chrI   chrII  chrIII   chrIV   chrIX ...  chrXII chrXIII  chrXIV   chrXV  chrXVI
    230218  813184  316620 1531933  439888 ... 1078177  924431  784333 1091291  948066

[Devon Ryan]

Are the seqlengths of D784G and txdb the same? I've never actually seen warnings about negative coordinates. Presuming you don't actually have any I don't know off-hand what's causing that.

[dktarathym]

The seqlengths were same.

[Devon Ryan]

No clue then. I'd have to go through the source code or try it myself. Perhaps post this on the bioconductor board.