text: user16764: I have 5609 chromosome positions with both ref and alt alleles. I want to retrieve rsIDs for the same. I tried get_rsid_from_position() of the MRutils package in R, but after some time while fetching data from the internet, the cache memory of my system got full, and it froze the system.
  Any other way to resolve this issue?
  I have 200 GB allotted for the cache memory.
  
  user475: An alternative possibility in R is using the library biomaRt from Bioconductor. Here an example starting from a table with 3 columns: Chr, Start, End. Organism is human and positions are assumed to be based on the reference version GRCh38.
  library(biomaRt)
  snpMart = useEnsembl(biomart = "snps", 
           dataset = "hsapiens_snp")
  
  # assuming your table is tab-separated, with column names
  myData <- read.table("myTable.txt", sep="\t", header=True)
  
  coords <- apply(myData, 1, paste, collapse = ":")
  
  
  # submit the query
  getBM(attributes = c('refsnp_id', 'chr_name', 'chrom_start', 'chrom_end', 'allele'),
  filters = c('chromosomal_region'), 
  values = coords, 
  mart = snpMart)  
  
  Source
  
original_text: 16764: <p>I have 5609 chromosome positions with both ref and alt alleles. I want to retrieve rsIDs for the same. I tried <code>get_rsid_from_position()</code> of the <code>MRutils</code> package in R, but after some time while fetching data from the internet, the cache memory of my system got full, and it froze the system.
  Any other way to resolve this issue?</p>
  <p>I have 200 GB allotted for the cache memory.</p>
   475: <p>An alternative possibility in R is using the library biomaRt from Bioconductor. Here an example starting from a table with 3 columns: Chr, Start, End. Organism is human and positions are assumed to be based on the reference version GRCh38.</p>
  <pre><code>library(biomaRt)
  snpMart = useEnsembl(biomart = &quot;snps&quot;, 
           dataset = &quot;hsapiens_snp&quot;)
  
  # assuming your table is tab-separated, with column names
  myData &lt;- read.table(&quot;myTable.txt&quot;, sep=&quot;\t&quot;, header=True)
  
  coords &lt;- apply(myData, 1, paste, collapse = &quot;:&quot;)
  
  
  # submit the query
  getBM(attributes = c('refsnp_id', 'chr_name', 'chrom_start', 'chrom_end', 'allele'),
  filters = c('chromosomal_region'), 
  values = coords, 
  mart = snpMart)  
  </code></pre>
  <p><a href="https://support.bioconductor.org/p/133105/" rel="nofollow noreferrer">Source</a></p>
  