SNPs distribution plot

Joanna_trinh · 05-14-2015, 11:59 AM

Anyone help me to draw SNPs density of 100kb windows from VCF file.

Thanks!

mediator · 05-14-2015, 02:48 PM

Open the VCF file in the latest version of IGV, then zoom out until your desired interval. You can then save the image as PNG or SVG.

Richard Finney · 05-14-2015, 02:53 PM

Try UCSC genome browser. It handles VCF files as a custom track ...

http://genome.ucsc.edu/cgi-bin/hgCustom (specify your genome and build ). This link may not
work if you haven't visited the UCSC page before. It needs some cookie variables set first.

This is the "add custom tracks" button available from the hgTracks page at the UCSC genome browser site.
Just google "UCSC genome browser " and go browse your favourite genome to set up your UCSC specific cookies.

http://i.imgur.com/CHWTU16.png

Joanna_trinh · 05-14-2015, 09:39 PM

Thanks all, but I want to create a plot like the below image...

Richard Finney · 05-15-2015, 07:12 AM

"squish" mode for your custom UCSC track should do that

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Plot distribution of length of sequences	noha osman	Introductions	1	03-31-2015 05:12 PM
How to read information from a kmer-distribution plot before denovo assembly	skblazer	Bioinformatics	1	01-13-2015 10:19 AM
How to draw the plot of SNV distribution	lipeiqiang	Bioinformatics	0	05-13-2014 02:17 AM
plot coverage distribution	meher	Bioinformatics	0	11-30-2012 11:37 AM
frequency distribution plot	alessandra85	Bioinformatics	5	01-19-2011 07:11 AM

05-14-2015, 11:59 AM	#1
Joanna_trinh Junior Member Location: Vietnam Join Date: Apr 2015 Posts: 3	SNPs distribution plot Anyone help me to draw SNPs density of 100kb windows from VCF file. Thanks!

05-14-2015, 02:53 PM	#3
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	Try UCSC genome browser. It handles VCF files as a custom track ... http://genome.ucsc.edu/cgi-bin/hgCustom (specify your genome and build ). This link may not work if you haven't visited the UCSC page before. It needs some cookie variables set first. This is the "add custom tracks" button available from the hgTracks page at the UCSC genome browser site. Just google "UCSC genome browser " and go browse your favourite genome to set up your UCSC specific cookies. http://i.imgur.com/CHWTU16.png Last edited by Richard Finney; 05-14-2015 at 06:33 PM.

05-14-2015, 02:48 PM	#2
mediator Member Location: New England Join Date: Nov 2010 Posts: 27	Open the VCF file in the latest version of IGV, then zoom out until your desired interval. You can then save the image as PNG or SVG.

05-15-2015, 07:12 AM	#5
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	"squish" mode for your custom UCSC track should do that