Question: SNP extraction from SNPlocs.Hsapiens.dbSNP144.GRCh38
0
gravatar for y-kuwahara
3.5 years ago by
y-kuwahara0
Japan
y-kuwahara0 wrote:

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   

 

 

dbsnp • 674 views
ADD COMMENTlink modified 3.5 years ago by Hervé Pagès ♦♦ 13k • written 3.5 years ago by y-kuwahara0
Answer: SNP extraction from SNPlocs.Hsapiens.dbSNP144.GRCh38
2
gravatar for Hervé Pagès
3.5 years ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:

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.gzds_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.

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Hervé Pagès ♦♦ 13k

Hi Herve,

 

Thanks for your response.

It would be very helpful and I could find the SNPs in ds_flat_chMulti.flat.gz file.

I hope you will update SNPlocs packages.

Thank you for your help,

Yusuke

ADD REPLYlink written 3.5 years ago by y-kuwahara0

I'll take a shot at this. That won't happen before January though...

H.

ADD REPLYlink written 3.5 years ago by Hervé Pagès ♦♦ 13k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 340 users visited in the last hour