[Patchwork-commits] r155 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin pkg/patchwork/man www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jan 4 11:48:00 CET 2013
Author: sebastian_d
Date: 2013-01-04 11:48:00 +0100 (Fri, 04 Jan 2013)
New Revision: 155
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
pkg/patchwork/man/karyotype_check.Rd
pkg/patchwork/man/patchwork.Medians_n_AI.Rd
pkg/patchwork/man/patchwork.plot.Rd
www/pw_exec.php
Log:
some documentation updates aswell as homepage updates
Modified: .git/COMMIT_EDITMSG
===================================================================
--- .git/COMMIT_EDITMSG 2013-01-04 10:24:05 UTC (rev 154)
+++ .git/COMMIT_EDITMSG 2013-01-04 10:48:00 UTC (rev 155)
@@ -1 +1 @@
-update to patchwork.alleledata function in patchwork. Also updated documentation for mpileup usage
+some documentation updates aswell as homepage updates
Modified: .git/index
===================================================================
(Binary files differ)
Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD 2013-01-04 10:24:05 UTC (rev 154)
+++ .git/logs/HEAD 2013-01-04 10:48:00 UTC (rev 155)
@@ -23,3 +23,4 @@
ac036caf16d37514a79e980f6da0e562c404bf57 eb98d72bfc02cfe4a0b30f1a2a0a64107444e40a Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1354267289 +0100 commit: Commented out assignAI which shouldent have been in use from patchwork
eb98d72bfc02cfe4a0b30f1a2a0a64107444e40a c7cdeb76a91652d654a622c343d9d40a38d673bb Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1354272864 +0100 commit: more fixes regarding assignAI
c7cdeb76a91652d654a622c343d9d40a38d673bb 684bd069c85e2e51e3e570ea00e9b586993e694b Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1357295102 +0100 commit: update to patchwork.alleledata function in patchwork. Also updated documentation for mpileup usage
+684bd069c85e2e51e3e570ea00e9b586993e694b 53e574e96950a119539b737b489262ce265a1c72 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1357296550 +0100 commit: some documentation updates aswell as homepage updates
Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master 2013-01-04 10:24:05 UTC (rev 154)
+++ .git/logs/refs/heads/master 2013-01-04 10:48:00 UTC (rev 155)
@@ -23,3 +23,4 @@
ac036caf16d37514a79e980f6da0e562c404bf57 eb98d72bfc02cfe4a0b30f1a2a0a64107444e40a Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1354267289 +0100 commit: Commented out assignAI which shouldent have been in use from patchwork
eb98d72bfc02cfe4a0b30f1a2a0a64107444e40a c7cdeb76a91652d654a622c343d9d40a38d673bb Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1354272864 +0100 commit: more fixes regarding assignAI
c7cdeb76a91652d654a622c343d9d40a38d673bb 684bd069c85e2e51e3e570ea00e9b586993e694b Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1357295102 +0100 commit: update to patchwork.alleledata function in patchwork. Also updated documentation for mpileup usage
+684bd069c85e2e51e3e570ea00e9b586993e694b 53e574e96950a119539b737b489262ce265a1c72 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1357296550 +0100 commit: some documentation updates aswell as homepage updates
Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master 2013-01-04 10:24:05 UTC (rev 154)
+++ .git/logs/refs/remotes/origin/master 2013-01-04 10:48:00 UTC (rev 155)
@@ -23,3 +23,4 @@
ac036caf16d37514a79e980f6da0e562c404bf57 eb98d72bfc02cfe4a0b30f1a2a0a64107444e40a Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1354267311 +0100 update by push
eb98d72bfc02cfe4a0b30f1a2a0a64107444e40a c7cdeb76a91652d654a622c343d9d40a38d673bb Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1354272883 +0100 update by push
c7cdeb76a91652d654a622c343d9d40a38d673bb 684bd069c85e2e51e3e570ea00e9b586993e694b Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1357295117 +0100 update by push
+684bd069c85e2e51e3e570ea00e9b586993e694b 53e574e96950a119539b737b489262ce265a1c72 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1357296561 +0100 update by push
Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master 2013-01-04 10:24:05 UTC (rev 154)
+++ .git/refs/heads/master 2013-01-04 10:48:00 UTC (rev 155)
@@ -1 +1 @@
-684bd069c85e2e51e3e570ea00e9b586993e694b
+53e574e96950a119539b737b489262ce265a1c72
Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master 2013-01-04 10:24:05 UTC (rev 154)
+++ .git/refs/remotes/origin/master 2013-01-04 10:48:00 UTC (rev 155)
@@ -1 +1 @@
-684bd069c85e2e51e3e570ea00e9b586993e694b
+53e574e96950a119539b737b489262ce265a1c72
Modified: pkg/patchwork/man/karyotype_check.Rd
===================================================================
--- pkg/patchwork/man/karyotype_check.Rd 2013-01-04 10:24:05 UTC (rev 154)
+++ pkg/patchwork/man/karyotype_check.Rd 2013-01-04 10:48:00 UTC (rev 155)
@@ -37,8 +37,8 @@
Copy number.
}
\item{mCn}{
- mCn.
- }
+ Minor Copy Number
+ }
\item{t}{
A list between int and ai.
}
Modified: pkg/patchwork/man/patchwork.Medians_n_AI.Rd
===================================================================
--- pkg/patchwork/man/patchwork.Medians_n_AI.Rd 2013-01-04 10:24:05 UTC (rev 154)
+++ pkg/patchwork/man/patchwork.Medians_n_AI.Rd 2013-01-04 10:48:00 UTC (rev 155)
@@ -8,7 +8,7 @@
}
\description{
-description
+Computes medians and Allelic imbalance for segments of the input genome.
}
\usage{
@@ -28,7 +28,7 @@
}
\details{
-Details
+See homepage at http://patchwork.r-forge.r-project.org/ for more information.
}
%\value{
Modified: pkg/patchwork/man/patchwork.plot.Rd
===================================================================
--- pkg/patchwork/man/patchwork.plot.Rd 2013-01-04 10:24:05 UTC (rev 154)
+++ pkg/patchwork/man/patchwork.plot.Rd 2013-01-04 10:48:00 UTC (rev 155)
@@ -28,17 +28,21 @@
}
\item{Tumor.pileup}{
Pileup file generated by either
- (SAMtools v 0.1.16 or older)
+ (SAMtools v 0.1.16 or older) \cr
samtools -vcf reference.fasta tumor.bam > outfile
- or (SAMtools v 0.1.17 or newer)
+ or (SAMtools v 0.1.17 or newer) \cr
samtools mpileup -f reference.fasta tumor.bam > outfile
}
\item{Tumor.vcf}{
Default is NULL.
- If samtools mpileup command has been used you will need to generate a vcf file using
- samtools mpileup -uf reference.fasta tumor.bam | bcftools view -bvcg - > raw.bcf
- and then
- bcftools view raw.bcf | vcfutils.pl varFilter -D100 > outfile.vcf
+ If samtools mpileup command has been used you will need to generate a vcf file using \cr
+ \cr
+ samtools mpileup -uf reference.fasta tumor.bam | bcftools view -bvcg - > raw.bcf \cr
+ \cr
+ and then \cr
+ \cr
+ bcftools view raw.bcf | vcfutils.pl varFilter -D100 > outfile.vcf \cr
+ \cr
Where the -D100 option filters out SNPs with a read depth higher than 100. It should be changed
depending on coverage, at 30x -D100 should be ok and at 120x -D500 might be more suitable for example.
}
@@ -104,7 +108,7 @@
%}
\author{
-Markus Mayrhofer, \email{markus.mayrhofer at medsci.uu.se}
+Markus Mayrhofer, \email{markus.mayrhofer at medsci.uu.se} \cr
Sebastian DiLorenzo, \email{sebastian.dilorenzo at medsci.uu.se}
}
%\note{
Modified: www/pw_exec.php
===================================================================
--- www/pw_exec.php 2013-01-04 10:24:05 UTC (rev 154)
+++ www/pw_exec.php 2013-01-04 10:48:00 UTC (rev 155)
@@ -46,9 +46,17 @@
or (SAMtools v 0.1.17 or newer)
samtools mpileup -f reference.fasta tumor.bam > outfile
- Tumor.vcf: Default is NULL. If samtools mpileup command has been used
- you will need to generate a vcf file using
- samtools mpileup -uf reference.fasta tumor.bam | bcftools view -vcg - > outfile.vcf
+ Tumor.vcf: Default is NULL. If samtools mpileup command has been used
+ you will need to generate a vcf file using
+ samtools mpileup -uf reference.fasta tumor.bam | bcftools
+ view -bvcg - > raw.bcf
+ and then
+ bcftools view raw.bcf | vcfutils.pl varFilter -D100 >
+ outfile.vcf
+ Where the -D100 option filters out SNPs with a read depth
+ higher than 100. It should be changed depending on coverage,
+ at 30x -D100 should be ok and at 120x -D500 might be more
+ suitable for example.
Normal.bam: Default is NULL. The matched normal sample of the your
Tumor.bam.
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