[Patchwork-commits] r151 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin www

[noreply at r-forge.r-project.org]

Author: sebastian_d
Date: 2012-11-15 13:51:14 +0100 (Thu, 15 Nov 2012)
New Revision: 151

Modified:
   .git/COMMIT_EDITMSG
   .git/index
   .git/logs/HEAD
   .git/logs/refs/heads/master
   .git/logs/refs/remotes/origin/master
   .git/refs/heads/master
   .git/refs/remotes/origin/master
   www/cg_inst.php
   www/pw_requ.php
Log:
small homepage changes

Modified: .git/COMMIT_EDITMSG
===================================================================
--- .git/COMMIT_EDITMSG	2012-11-14 16:16:52 UTC (rev 150)
+++ .git/COMMIT_EDITMSG	2012-11-15 12:51:14 UTC (rev 151)
@@ -1 +1 @@
-updates to homepage regarding mpileup,vcfs and filtering
+small homepage changes

Modified: .git/index
===================================================================
(Binary files differ)

Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD	2012-11-14 16:16:52 UTC (rev 150)
+++ .git/logs/HEAD	2012-11-15 12:51:14 UTC (rev 151)
@@ -19,3 +19,4 @@
 0ea92759a953e9e176617cf22b4050ce2fed0bef 0de5cb34cc64ebefb98b257d93c88bfd65c7f640 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1347370308 +0200	commit: Updated homepage info
 0de5cb34cc64ebefb98b257d93c88bfd65c7f640 53fb1e3cd198d3f12e30ab52891a42e19f5bfdfc Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1348837295 +0200	commit: updated to reflect that bz2 mastervar files will also work to homepage
 53fb1e3cd198d3f12e30ab52891a42e19f5bfdfc 121e1229bbfdb5e93aea7268469f568c16388ada Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1352909758 +0100	commit: updates to homepage regarding mpileup,vcfs and filtering
+121e1229bbfdb5e93aea7268469f568c16388ada ac036caf16d37514a79e980f6da0e562c404bf57 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1352983874 +0100	commit: small homepage changes

Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master	2012-11-14 16:16:52 UTC (rev 150)
+++ .git/logs/refs/heads/master	2012-11-15 12:51:14 UTC (rev 151)
@@ -19,3 +19,4 @@
 0ea92759a953e9e176617cf22b4050ce2fed0bef 0de5cb34cc64ebefb98b257d93c88bfd65c7f640 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1347370308 +0200	commit: Updated homepage info
 0de5cb34cc64ebefb98b257d93c88bfd65c7f640 53fb1e3cd198d3f12e30ab52891a42e19f5bfdfc Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1348837295 +0200	commit: updated to reflect that bz2 mastervar files will also work to homepage
 53fb1e3cd198d3f12e30ab52891a42e19f5bfdfc 121e1229bbfdb5e93aea7268469f568c16388ada Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1352909758 +0100	commit: updates to homepage regarding mpileup,vcfs and filtering
+121e1229bbfdb5e93aea7268469f568c16388ada ac036caf16d37514a79e980f6da0e562c404bf57 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1352983874 +0100	commit: small homepage changes

Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master	2012-11-14 16:16:52 UTC (rev 150)
+++ .git/logs/refs/remotes/origin/master	2012-11-15 12:51:14 UTC (rev 151)
@@ -19,3 +19,4 @@
 0ea92759a953e9e176617cf22b4050ce2fed0bef 0de5cb34cc64ebefb98b257d93c88bfd65c7f640 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1347370323 +0200	update by push
 0de5cb34cc64ebefb98b257d93c88bfd65c7f640 53fb1e3cd198d3f12e30ab52891a42e19f5bfdfc Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1348837313 +0200	update by push
 53fb1e3cd198d3f12e30ab52891a42e19f5bfdfc 121e1229bbfdb5e93aea7268469f568c16388ada Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1352909786 +0100	update by push
+121e1229bbfdb5e93aea7268469f568c16388ada ac036caf16d37514a79e980f6da0e562c404bf57 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1352983892 +0100	update by push

Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master	2012-11-14 16:16:52 UTC (rev 150)
+++ .git/refs/heads/master	2012-11-15 12:51:14 UTC (rev 151)
@@ -1 +1 @@
-121e1229bbfdb5e93aea7268469f568c16388ada
+ac036caf16d37514a79e980f6da0e562c404bf57

Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master	2012-11-14 16:16:52 UTC (rev 150)
+++ .git/refs/remotes/origin/master	2012-11-15 12:51:14 UTC (rev 151)
@@ -1 +1 @@
-121e1229bbfdb5e93aea7268469f568c16388ada
+ac036caf16d37514a79e980f6da0e562c404bf57

Modified: www/cg_inst.php
===================================================================
--- www/cg_inst.php	2012-11-14 16:16:52 UTC (rev 150)
+++ www/cg_inst.php	2012-11-15 12:51:14 UTC (rev 151)
@@ -1,5 +1,6 @@
 PatchworkCG works on Unix (Linux, Ubuntu, MacOSX, etc) based systems. You will probably get an error
-when trying to install it on Windows, and you definitely can't run it.
+when trying to install it on Windows. If you get it to work on Windows send us an email and
+let us know, we have not tested it.
 <br /><br />
 
 Begin by starting R. It is recommended that you use the latest version.

Modified: www/pw_requ.php
===================================================================
--- www/pw_requ.php	2012-11-14 16:16:52 UTC (rev 150)
+++ www/pw_requ.php	2012-11-15 12:51:14 UTC (rev 151)
@@ -39,7 +39,8 @@
 <br />
 
 The optional VCF files need to be supplied if you are using a later version of samtools and have opted
-for using samtools mpileup to create the pileup file as they contain consensus and variant information.
+for using samtools mpileup to create the pileup file. The vcfs contain consensus and variant information which
+the mpileup generated pileup lacks.
 More information on this is farther down.<br /><br />
 
 Here are two standard reference files created for patchwork for samples where alignment used the UCSC HG19 reference.
@@ -157,20 +158,22 @@
 To mpileup either your normal sample or tumor sample BAM files: <br />
 
 <pre>
-	samtools mpileup -f <humangenome>.fasta <tumor_or_normalfile>.bam > mpileup
+	samtools mpileup -f <humangenome>.fasta <tumor_or_normal>.bam > mpileup
 </pre>
 
 For consensus calling: <br />
 
 <pre>
-	samtools mpileup -uf <humangenome>.fasta <tumor_or_normalfile>.bam | bcftools view -bvcg - > <unfiltered_output>.bcf
+	samtools mpileup -uf <humangenome>.fasta <tumor_or_normal>.bam |
+		bcftools view -bvcg - > <unfiltered_output>.bcf
 
 	bcftools view <unfiltered_output>.bcf | vcfutils.pl varFilter -D100 > <output>.vcf
 </pre>
 
 The -D100 option filters out SNPs that had read depth higher than 100,
 (They might be from repeat regions in your sample.) you should change this parameter based on the kind of coverage 
-your sample has. For average coverage 30x =~ -D100, average coverage 120x =~ -D500 etc. <br /><br />
+your sample has.<br />
+For average coverage 30x =~ -D100, average coverage 120x =~ -D500 etc. <br /><br />
 
 Remember to use both of these files when running patchwork.plot() with the vcf file in the Tumor.vcf/Normal.vcf parameter
  and the mpileup in Tumor.pileup/Normal.pileup parameter. <br /><br />