Variant Annotation in R

Question

[adakoury]

I am trying to perform Variant Annotation using "VariantAnnotation" in R I was trying to make TxDb file form Gff file but I got a warning messages as shown below. I am wondering if anybody has gone into the same problem and how it was solved.

> txdb <- makeTxDbFromGFF(gtffile, format= "gtf",circ_seqs=character())
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning messages:
1: In .local(con, format, text, ...) :
  gff-version directive indicates version is 3, not 2
2: In .extract_transcripts_from_GRanges(tx_IDX, gr, type, ID, Name) :
  The following transcripts have multiple parts that were merged:
3: Named parameters not used in query: internal_chrom_id, chrom, length, is_circular

[WouterDeCoster]

A warning is not an error, so if for the rest everything goes fine with the rest of your commands then this isn't something to worry about.

[adakoury]

Here is the whole process. The outcome was not something I was expecting. Any idea where I amde a mistake or missed something.

> vcf <- readVcf("chroA01.vcf", "Brassica_napus.annotation_v5_sorted_modified.gff")
> vcf
class: CollapsedVCF 
dim: 11847 189 
rowRanges(vcf):
  GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER
info(vcf):
  DataFrame with 3 columns: NS, DP, AF
info(header(vcf)):
      Number Type    Description                
   NS 1      Integer Number of Samples With Data
   DP 1      Integer Total Depth                
   AF .      Float   Allele Frequency           
geno(vcf):
  SimpleList of length 5: GT, AD, DP, GQ, PL
geno(header(vcf)):
      Number Type    Description                                               
   GT 1      String  Genotype                                                  
   AD .      Integer Allelic depths for the reference and alternate alleles ...
   DP 1      Integer Read Depth (only filtered reads used for calling)         
   GQ 1      Float   Genotype Quality                                          
   PL 3      Float   Normalized, Phred-scaled likelihoods for AA,AB,BB genot...
> gtffile <- file.path("K:/ClubrootGenetics/Reference genomes/B. napus reference genome v5/modified files/Brassica_napus.annotation_v5_sorted_modified.gff")
> txdb <- makeTxDbFromGFF(gtffile, format= "gtf",circ_seqs=character())
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning messages:
1: In .local(con, format, text, ...) :
  gff-version directive indicates version is 3                                                          , not 2
2: In .extract_transcripts_from_GRanges(tx_IDX, gr, type, ID, Name) :
  The following transcripts have multiple parts that were merged:
3: Named parameters not used in query: internal_chrom_id, chrom, length, is_circular 
> seqlevels(vcf) <- "chrA01"
> rd <- rowRanges(vcf)
> loc <- locateVariants(rd, txdb, CodingVariants())
>  head(loc, 3)
GRanges object with 0 ranges and 9 metadata columns:
   seqnames    ranges strand | LOCATION  LOCSTART    LOCEND   QUERYID      TXID
      <Rle> <IRanges>  <Rle> | <factor> <integer> <integer> <integer> <integer>
           CDSID      GENEID       PRECEDEID        FOLLOWID
   <IntegerList> <character> <CharacterList> <CharacterList>
  -------
  seqinfo: no sequences

[GenoMax]

Hint: Highlight text and then use the "101" button to format code/output to make it readable.

[adakoury]

Which text do you refere to?

[GenoMax]

e.g. from your previous post everything from >vcf ..... seqinfo: no sequences.

[adakoury]

I did. Is it readable now?

[WouterDeCoster]

You could check if the variables gtffile, txdb and rd look "as expected" to figure out which step went wrong.

[adakoury]

I solved the problem. there was an error in the gff file.