Changes

10. Figure out which steps to run first.  The steps go in the order glfN, vcfN, pvcfN, filtN, svmN, splitN, allN where N is the name of a chromosome (ie, 1-22 and maybe X and Y).  If you skip a step, it's not a problem, because <code>make</code> will run it for you.  If you're confident that everything will work beautifully, you can go straight to the step <code>allN</code> (or just <code>all</code> as a shortcut).

10. Figure out which steps to run first.  The steps go in the order glfN, vcfN, pvcfN, filtN, svmN, splitN, allN where N is the name of a chromosome (ie, 1-22 and maybe X and Y).  If you skip a step, it's not a problem, because <code>make</code> will run it for you.  If you're confident that everything will work beautifully, you can go straight to the step <code>allN</code> (or just <code>all</code> as a shortcut).

:* For example, I used <code>glf1 glf2 glf3 glf4 glf5 glf6 glf7 glf8 glf9 glf10 glf11 glf12 glf13 glf14 glf15 glf16 glf17 glf18 glf19 glf20 glf21 glf22 </code> the first time I ran on Flux.  Then I ran <code>vcf1 vcf2...<code>, and on down the list until finally <code>all</code>.

:* For example, I used <code>glf1 glf2 glf3 glf4 glf5 glf6 glf7 glf8 glf9 glf10 glf11 glf12 glf13 glf14 glf15 glf16 glf17 glf18 glf19 glf20 glf21 glf22 </code> the first time I ran on Flux.  Then I ran <code>vcf1 vcf2...</code>, and on down the list until finally <code>all</code>.

:* Feel free to use the script <code>perl -e 'print "glf$_ " for 1..22'</code> to mitigate repetitive strain injuries.

:* Feel free to use the script <code>perl -e 'print "glf$_ " for 1..22'</code> to mitigate repetitive strain injuries.