Answers.Body: <p>Yes, if you load the list you are interested in as a non-indexed "BED" file then you can jump to an rsID or any other name in the BED file. You'll need a targeted list, dbSNP for example is much too large to load in this way.</p>
  
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Answers.Text: Great, thank. Is there an hg38 bed file with the rsIDs of one of the 1M SNP arrays out in the market?
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Answers.UserDisplayName: Jim Robinson
Answers.Body: <p>If you want all rsIDs (complete dbSnp database) then Pierre's answer is the best option currently.    Any bed file with all the rsIDs would be too big to load.  For a targeted list of, say, 100,000 or fewer snps you can use a bed file.  </p>
  
  <p>BTW igv.js already does the equivalent of Pierre's suggestion, this will be ported to IGV desktop in the near future.  </p>
  
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Answers.UserDisplayName: Jim Robinson
Answers.Body: <p>you can use mysql ucsc to get the position of the SNP and then ask IGV to take some picures: see <a href="https://software.broadinstitute.org/software/igv/batch" rel="nofollow noreferrer">https://software.broadinstitute.org/software/igv/batch</a></p>
  
  <pre><code>$ echo -e 'rs66823261\nrs25' | awk '{printf("select concat(chrom,\":\",chromStart-10,\"-\",chromEnd+10) from  snp150 where name=\"%s\";\n",$1);}' | mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -D hg38 -N | awk '{printf("goto %s\nsnapshot\n",$1);}'
  
  goto chr8:170681-170702
  snapshot
  goto chr7:11584131-11584152
  snapshot
  </code></pre>
  
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Body: <p>Is it possible to load a list of rsID identifiers (e.g. rs66823261) to IGV to then be able to jump to the location of each of them when copy+pasting the rsID on the locus text box?</p>
  
  <p>For human and other genomes, there is currently the feature of typing in a gene name, then jumping to the gene location.</p>
  
  <p>I wonder if there is a way of achieving the same for rsIDs.</p>
  
  <p>EDIT: thanks for the answers so far. I downloaded the Infinium GSA bed file from Illumina's website (<a href="https://support.illumina.com/downloads/infinium-global-screening-array-v1-0-support-files.html" rel="nofollow noreferrer">https://support.illumina.com/downloads/infinium-global-screening-array-v1-0-support-files.html</a>), loaded on an IGV session, which asked to create an index. I did a liftover of the file to hg38 and sorted with bedtools sort. Then I went to the text box, introduced one of the rs ids:</p>
  
  <p>rs6569648</p>
  
  <p>Got a positive result. Thank you all!</p>
  
Tags: <snp><igv>
Title: IGV jump to rsID location
ThreadText: # IGV jump to rsID location
  
  (Asked by: username_0 on 2017-10-25)
  
  Is it possible to load a list of rsID identifiers (e.g. rs66823261) to IGV to then be able to jump to the location of each of them when copy+pasting the rsID on the locus text box?
  
  For human and other genomes, there is currently the feature of typing in a gene name, then jumping to the gene location.
  
  I wonder if there is a way of achieving the same for rsIDs.
  
  EDIT: thanks for the answers so far. I downloaded the Infinium GSA bed file from Illumina's website (<https://support.illumina.com/downloads/infinium-global-screening-array-v1-0-support-files.html>), loaded on an IGV session, which asked to create an index. I did a liftover of the file to hg38 and sorted with bedtools sort. Then I went to the text box, introduced one of the rs ids:
  
  rs6569648
  
  Got a positive result. Thank you all!
  
  **Tags:** snp, igv
  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_1 on 2017-10-25. Score: 2 | Accepted answer
  
  Yes, if you load the list you are interested in as a non-indexed "BED" file then you can jump to an rsID or any other name in the BED file. You'll need a targeted list, dbSNP for example is much too large to load in this way.
  
  > **Comments:**
  > **username_0**: Great, thank. Is there an hg38 bed file with the rsIDs of one of the 1M SNP arrays out in the market?  
  
  ---
  
  ### Answer by username_1 on 2017-10-26. Score: 0
  
  If you want all rsIDs (complete dbSnp database) then username_2's answer is the best option currently. Any bed file with all the rsIDs would be too big to load. For a targeted list of, say, 100,000 or fewer snps you can use a bed file.
  
  BTW igv.js already does the equivalent of username_2's suggestion, this will be ported to IGV desktop in the near future.
  
  
  ---
  
  ### Answer by username_2 on 2017-10-26. Score: 0
  
  you can use mysql ucsc to get the position of the SNP and then ask IGV to take some picures: see <https://software.broadinstitute.org/software/igv/batch>
  
  ```
  $ echo -e 'rs66823261\nrs25' | awk '{printf("select concat(chrom,\":\",chromStart-10,\"-\",chromEnd+10) from  snp150 where name=\"%s\";\n",$1);}' | mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -D hg38 -N | awk '{printf("goto %s\nsnapshot\n",$1);}'
  
  goto chr8:170681-170702
  snapshot
  goto chr7:11584131-11584152
  snapshot
  
  ```
  
  
  ---
  
  