[Patchwork-commits] r150 - .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
noreply at r-forge.r-project.org
Wed Nov 14 17:16:52 CET 2012
Author: sebastian_d
Date: 2012-11-14 17:16:52 +0100 (Wed, 14 Nov 2012)
New Revision: 150
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/index.php
www/pw_inst.php
www/pw_requ.php
Log:
update homepage information regarding mpileup, vcfs and filtering
Modified: .git/COMMIT_EDITMSG
===================================================================
--- .git/COMMIT_EDITMSG 2012-09-28 13:02:29 UTC (rev 149)
+++ .git/COMMIT_EDITMSG 2012-11-14 16:16:52 UTC (rev 150)
@@ -1 +1 @@
-updated to reflect that bz2 mastervar files will also work to homepage
+updates to homepage regarding mpileup,vcfs and filtering
Modified: .git/index
===================================================================
(Binary files differ)
Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD 2012-09-28 13:02:29 UTC (rev 149)
+++ .git/logs/HEAD 2012-11-14 16:16:52 UTC (rev 150)
@@ -18,3 +18,4 @@
d5df007a35dcbf109f45dd0c15d100996ee41b9b 0ea92759a953e9e176617cf22b4050ce2fed0bef Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1346421578 +0200 commit: updated changelog and description
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
Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master 2012-09-28 13:02:29 UTC (rev 149)
+++ .git/logs/refs/heads/master 2012-11-14 16:16:52 UTC (rev 150)
@@ -18,3 +18,4 @@
d5df007a35dcbf109f45dd0c15d100996ee41b9b 0ea92759a953e9e176617cf22b4050ce2fed0bef Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1346421578 +0200 commit: updated changelog and description
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
Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master 2012-09-28 13:02:29 UTC (rev 149)
+++ .git/logs/refs/remotes/origin/master 2012-11-14 16:16:52 UTC (rev 150)
@@ -18,3 +18,4 @@
d5df007a35dcbf109f45dd0c15d100996ee41b9b 0ea92759a953e9e176617cf22b4050ce2fed0bef Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1346421591 +0200 update by push
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
Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master 2012-09-28 13:02:29 UTC (rev 149)
+++ .git/refs/heads/master 2012-11-14 16:16:52 UTC (rev 150)
@@ -1 +1 @@
-53fb1e3cd198d3f12e30ab52891a42e19f5bfdfc
+121e1229bbfdb5e93aea7268469f568c16388ada
Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master 2012-09-28 13:02:29 UTC (rev 149)
+++ .git/refs/remotes/origin/master 2012-11-14 16:16:52 UTC (rev 150)
@@ -1 +1 @@
-53fb1e3cd198d3f12e30ab52891a42e19f5bfdfc
+121e1229bbfdb5e93aea7268469f568c16388ada
Modified: www/cg_inst.php
===================================================================
--- www/cg_inst.php 2012-09-28 13:02:29 UTC (rev 149)
+++ www/cg_inst.php 2012-11-14 16:16:52 UTC (rev 150)
@@ -1,3 +1,7 @@
+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.
+<br /><br />
+
Begin by starting R. It is recommended that you use the latest version.
<br /><br />
Modified: www/index.php
===================================================================
--- www/index.php 2012-09-28 13:02:29 UTC (rev 149)
+++ www/index.php 2012-11-14 16:16:52 UTC (rev 150)
@@ -232,7 +232,7 @@
<!-- End of StatCounter Code for Default Guide -->
<div style="display:inline-block; width:2px; height:1px;"></div>
<!-- LAST MODIFIED -->
- Last modified: 2012-09-11
+ Last modified: 2012-11-14
</div>
Modified: www/pw_inst.php
===================================================================
--- www/pw_inst.php 2012-09-28 13:02:29 UTC (rev 149)
+++ www/pw_inst.php 2012-11-14 16:16:52 UTC (rev 150)
@@ -1,3 +1,7 @@
+Patchwork 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.
+<br /><br />
+
Begin by starting R. It is recommended that you use the latest version.
<br /><br />
Modified: www/pw_requ.php
===================================================================
--- www/pw_requ.php 2012-09-28 13:02:29 UTC (rev 149)
+++ www/pw_requ.php 2012-11-14 16:16:52 UTC (rev 150)
@@ -11,9 +11,11 @@
<!-- <li>A Human Genome fasta file</li> -->
<li>An aligned and sorted BAM file of tumor content</li>
<li>A BAI index of your BAM file</li>
- <li>A Pileup of your BAM file</li>
+ <li>A pileup of your BAM file</li>
+ <li>(optional) A VCF file of your tumor pileup</li>
<li>(optional) A matched normal sample to your tumor in BAM format</li>
<li>(optional) A pileup of your normal sample BAM</li>
+ <li>(optional) A VCF file of your normal pileup</li>
<li>(optional) A BAI index of your normal sample BAM</li>
<li>(optional) A standard Reference file. (Illumina/Solexa, SOLiD or your own)</li>
</ul>
@@ -28,12 +30,18 @@
files. There is really no point in using all of them.
<br /><br />
If you have a matched normal sample you should make a pileup of this and use those two arguments.
+If you have a normal you should also create a BAI file of it, it will not be a parameter but is
+required for the file to be read by patchwork.
<br />
In some cases it may be better to use the reference file and a pileup.
<br />
You can also run patchwork.plot() with only a reference file.<br />
<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.
+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.
It is very important that you choose a reference which matches the sequencing technology and reference genome used on
your tumor sample.<br />
@@ -155,9 +163,15 @@
For consensus calling: <br />
<pre>
- samtools mpileup -uf <humangenome>.fasta <tumor_or_normalfile>.bam | bcftools view -vcg - > <output>.vcf
+ samtools mpileup -uf <humangenome>.fasta <tumor_or_normalfile>.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 />
+
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 />
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