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Old 05-14-2015, 11:59 AM   #1
Joanna_trinh
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Default SNPs distribution plot

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

Thanks!
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Old 05-14-2015, 02:48 PM   #2
mediator
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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.
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Old 05-14-2015, 02:53 PM   #3
Richard Finney
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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.
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Old 05-14-2015, 09:39 PM   #4
Joanna_trinh
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Thanks all, but I want to create a plot like the below image...
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File Type: jpg SNPs density.jpg (11.6 KB, 31 views)
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Old 05-15-2015, 07:12 AM   #5
Richard Finney
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"squish" mode for your custom UCSC track should do that
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