Hi,

I'm trying to extract all snps on TNF transcript from SNPlocs.Hsapiens.dbSNP144.GRCh38, but only one is returned (rs281865419). In the NCBI variation viewer, there are 255 snps.

Is my code right? And is there a better approach?

My code and sessionInfo are below.

Many thanks, 

Yusuke

----R-code----

library(SNPlocs.Hsapiens.dbSNP144.GRCh38);
library(TxDb.Hsapiens.UCSC.hg38.knownGene);
library(VariantAnnotation);

txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene;
tx.by.gene  <- transcriptsBy(txdb, "gene");

snps <- SNPlocs.Hsapiens.dbSNP144.GRCh38;
chr6 <- snpsBySeqname(snps, "ch6");

chr6 <- renameSeqlevels(chr6, sub("^chrMT", "chrM", sub("^ch", "chr", seqlevels(chr6))));
seqinfo(chr6)@genome <- rep("hg38", 25);

hit <- findOverlaps(chr6, tx.by.gene["7124"]); # EntrezID of TNF
chr6[hit@queryHits];

GRanges object with 1 range and 2 metadata columns:
      seqnames               ranges strand |   RefSNP_id alleles_as_ambig
         <Rle>            <IRanges>  <Rle> | <character>      <character>
  [1]     chr6 [31577157, 31577157]      + | rs281865419                Y
  -------
  seqinfo: 25 sequences (1 circular) from hg38 genome

sessionInfo()

R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] VariantAnnotation_1.14.1                
 [2] Rsamtools_1.20.4                        
 [3] TxDb.Hsapiens.UCSC.hg38.knownGene_3.1.2 
 [4] GenomicFeatures_1.20.6                  
 [5] AnnotationDbi_1.30.1                    
 [6] Biobase_2.28.0                          
 [7] SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.11
 [8] BSgenome_1.36.3                         
 [9] rtracklayer_1.28.4                      
[10] Biostrings_2.36.4                       
[11] XVector_0.8.0                           
[12] GenomicRanges_1.20.8                    
[13] GenomeInfoDb_1.4.3                      
[14] IRanges_2.2.9                           
[15] S4Vectors_0.6.6                         
[16] BiocGenerics_0.14.0   

Hi Yusuke,

The SNPlocs packages are made from the files ds_flat_ch1.flat.gz, ds_flat_ch2.flat.gz, ..., ds_flat_ch22.flat.gz, ds_flat_chX.flat.gz, ds_flat_chY.flat.gz, and ds_flat_chMT.flat.gz found at this location: http://ftp.ncbi.nih.gov/snp/organisms/human_9606/ASN1_flat

I think that most of the SNPs you see in the NCBI variation viewer for the TNF gene belong to the ds_flat_chMulti.flat.gz file.

I'll try to update the SNPlocs packages to also include SNPs from this file in the future.

Cheers,

H.