Hello!
I am using Variant Annotation package from Bioconductor to annotate my variant but it missed some variants in the output.
For example, in var I have the following mutation site :
CHROM POS REF ALT
9751 chr6 41184897 G A
I used GRanges for the genomic locations and their associated annotations:
gr <- GRanges(seqnames = var$CHROM, ranges = IRanges(as.numeric(var$POS), as.numeric(var$POS)), strand="*")
The output was:
GRanges object with 1 range and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr6 [41184897, 41184897] *
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
After that, I used locateVariants to annotate the sites:
gr_var <- locateVariants(gr, txdb, AllVariants(), ignore.strand=T)
where txdb is txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene (library of R).
But I obtained this output:
GRanges object with 0 ranges and 9 metadata columns:
seqnames ranges strand | LOCATION LOCSTART LOCEND QUERYID TXID CDSID GENEID PRECEDEID FOLLOWID
<Rle> <IRanges> <Rle> | <factor> <integer> <integer> <integer> <integer> <IntegerList> <character> <CharacterList> <CharacterList>
-------
seqinfo: no sequences
I searched the mutation site in genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr6%3A41184397-41185396&hgsid=612547501_yo5UeqjaPqdVW1X73qUXN4riW5iA and I found its genes: TREML3 (Entrez Gene ID: 340206)
Therefore, I looked into txdb if it was reported the 340206 gene ID:
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
exon_columns <- columns(txdb)
exon_columns <- exon_columns[which(exon_columns %in% c("EXONID", "EXONNAME", "GENEID"))]
all_exons <- exons(txdb, columns=exon_columns)
temp <- as.data.frame(all_exons)
temp[temp$GENEID == "340206", ]
And I found that the Gene_ID is included in txdb:
seqnames start end width strand EXONID EXONNAME GENEID
95166 chr6 41176292 41176892 601 - 95166 <NA> 340206
95167 chr6 41177337 41177468 132 - 95167 <NA> 340206
95168 chr6 41183500 41183557 58 - 95168 <NA> 340206
95169 chr6 41184865 41184915 51 - 95169 <NA> 340206
95170 chr6 41185391 41185685 295 - 95170 <NA> 340206
Do you have any suggestions as to how to solve?
Thank you in advance
Best
