This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Import A List Of Regions In Dgv And Get How Many Times We Have Deletions/Duplications In These Regions

Is there a simple way to import a list of regions(hg18) like below 

chr1:72794860-72856439
chr1:195005320-195066067
chr6:32605081-32633891

in DGV(database of Genomic Variants) and get how many times we have deletion or duplication in these regions?Thanks

cnv
• 2,015 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Omid Omid

thanks Pierre can I import a list of regions into DGV and get output?

• 0 views • link
written by Omid Omid

1 answer

You can download the data from http://projects.tcag.ca/variation/tableview.asp?table=DGV_Content_Summary.txt and count the regions using, for example, bedtools.

or you can use a simple command line:

curl -s "http://projects.tcag.ca/variation/downloads/variation.hg18.v10.nov.2010.txt" |\
cut -d '       ' -f 3,4,5,6  |\
awk -F '     ' '{if($1=="chr1" &&  !(int($2)>72856439 || int($3)< 72794860 )) { print ; } }' |\
cut -d '      ' -f 4 | sort | uniq -c

  3 CopyNumber
• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Log in to answer this question.

More posts like this