3

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!

719016
  • 2,324
  • 13
  • 19

3 Answers3

2

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.

Devon Ryan
  • 19,602
  • 2
  • 29
  • 60
Jim Robinson
  • 56
  • 1
  • Great, thank. Is there an hg38 bed file with the rsIDs of one of the 1M SNP arrays out in the market? – 719016 Oct 26 '17 at 09:33
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
Pierre
  • 1,536
  • 7
  • 11
0

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.

BTW igv.js already does the equivalent of Pierre's suggestion, this will be ported to IGV desktop in the near future.

Jim Robinson
  • 56
  • 1