Dear All,
I am making LD plots for r-square using 100G data that I downloaded with tabix, converted with VCF tools, and pushed into Haploview format using plink --recodeHV option.
I then did some LD pruning for my SNP of interest (also in plink)
I am trying to produce the plots on the command line but the output shows no marker names.
> java -Xmx8g -Djava.io.tmpdir=/dir/ -jar Haploview.jar -n -skipcheck \
> -pedfile ex.prunedHV.ped \
> -info ex.prunedHV.info \
> -png \
> -ldvalues RSQ \
> -ldcolorscheme RSQ \
> -out /outdir/ex.
If I add the commands to show infoTrack I get no output at all:
> -infoTrack \
> -chromosome 10 \
Just some error messages:
Exception in thread "main" java.awt.HeadlessException at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:159) at java.awt.Window.<init>(Window.java:431) at java.awt.Frame.<init>(Frame.java:403) at java.awt.Frame.<init>(Frame.java:368) at javax.swing.SwingUtilities$SharedOwnerFrame.<init>(SwingUtilities.java:1733) at javax.swing.SwingUtilities.getSharedOwnerFrame(SwingUtilities.java:1810) at javax.swing.JOptionPane.getRootFrame(JOptionPane.java:1673) at javax.swing.JOptionPane.showOptionDialog(JOptionPane.java:846) at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:650) at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:621) at edu.mit.wi.haploview.DPrimeDisplay.computePreferredSize(DPrimeDisplay.java:1417) at edu.mit.wi.haploview.DPrimeDisplay.computePreferredSize(DPrimeDisplay.java:1258) at edu.mit.wi.haploview.DPrimeDisplay.<init>(DPrimeDisplay.java:125) at edu.mit.wi.haploview.HaploText.processFile(HaploText.java:1677) at edu.mit.wi.haploview.HaploText.processTextOnly(HaploText.java:1369) at edu.mit.wi.haploview.HaploText.<init>(HaploText.java:245) at edu.mit.wi.haploview.HaploView.main(HaploView.java:1600)
Can anyone help me resolve this problem? Thank you
