Changes between Version 35 and Version 36 of se.lu.onk.BAFsegmentation

Timestamp:

Jun 1, 2010, 3:34:12 PM (14 years ago)

Author:

markus

Comment:

--

se.lu.onk.BAFsegmentation

@@ -10 +10 @@
 
 === News ===
- 
+
+ * Jun. 1, 2010. BAFsegmentation 1.2.0 release. Added support for paired tumor-normal samples. 
+
  * Mar. 13, 2009. BAFsegmentation 1.1.2 release. This is a minor bug-fix release. Fixed bugs include errors in documentation (default has never been to remove cnv probes), handling of when there are no probes for entire chromosomes, and 'split_samples.pl' can now handle language settings for which !BeadStudio generates files in which comma denotes the decimal point.
 
@@ -24 +26 @@
 === Future plans ===
 
- * Add support for using paired tumor-normal samples.
  * Adaptation of BAFsegmentation to samples having 100% tumor content, for example, cell-lines.
  * Integration of log R ratio into calling of regions and their type.
@@ -34 +35 @@
 === Download BAFsegmentation ===
 
-[http://cbbp.thep.lu.se/~markus/software/BAFsegmentation/BAFsegmentation-1.1.2.zip?format=raw Download the latest stand-alone release (BAFsegmentation 1.1.2).]
+[http://cbbp.thep.lu.se/~markus/software/BAFsegmentation/BAFsegmentation-1.2.0.zip?format=raw Download the latest stand-alone release (BAFsegmentation 1.2.0).]
 
 === Supplemental Data ===
@@ -71 +72 @@
   
 ''Input data format''
+  
+  __Unpaired samples__
+
   BAFsegmentation is applied to data for a set of samples in a file that should be tab-delimited in the following format:
   ||Name||Chr||Position||sample1.B Allele Freq||sample1.Log R Ratio||sample2.B Allele Freq||sample2.Log R Ratio||sample3.B Allele Freq||sample3.Log R Ratio||...|| 
@@ -84 +88 @@
   where ''example_beadstudio_data.txt'' is a file exported from !BeadStudio in the format described above. With some language settings !BeadStudio exports files with commas (,) as decimal points; 'split_samples.pl' replaces all commas (,) in data columns with points (.) in the 'split_samples.pl' results files.
 
-  This script will generate one file per sample together with a file ''sample_names.txt'' in the BAFsegmentation subdirectory ''extracted''. These files are used when BAFsegmentation is run and can be deleted once the samples are normalized.
+  This script will generate one file per sample together with a file ''sample_names.txt'' in the BAFsegmentation subdirectory ''extracted''. These files are used when BAFsegmentation is run and can be deleted once the samples are segmented.
+
+  __Paired tumor-normal samples__
+
+  BAFsegmentation can be applied to paired tumor-normal samples essentially as for unpaired samples. The main difference is that the genotypes for the normal samples are required. BAFsegmentation is applied to data for a set of paired tumor-normal samples in a file that should be tab-delimited in the following format:
+  ||Name||Chr||Position||sample1.GType || sample1.B Allele Freq||sample1.Log R Ratio||sample2.GType||sample2.B Allele Freq||sample2.Log R Ratio||...|| 
+  ||rs12354060||1||10004||AA||1||0.110391||AB||1||-0.05188531||...||
+  ||rs2691310||1||46844||AB||0.5519782||0.2984372||BB||0.4636427||0.3640218||...||
+  ||...||...||...||...||...||...||...||...||...||...||
+
+  For Illumina arrays data can be exported in this format directly from !BeadStudio. The data need to be split into a separate file for each sample using the script ''split_samples.pl''. In the BAFsegmentation directory, run ''split_samples.pl'' with the following command:
+
+  {{{  
+    perl split_samples.pl --data_file=example/example_beadstudio_paired_data.txt
+  }}}
+  where ''example_beadstudio_paired_data.txt'' is a file exported from !BeadStudio in the format described above. With some language settings !BeadStudio exports files with commas (,) as decimal points; 'split_samples.pl' replaces all commas (,) in data columns with points (.) in the 'split_samples.pl' results files.
+
+  This script will generate one file per sample together with a file ''sample_names.txt'' in the BAFsegmentation subdirectory ''extracted''. These files are used when BAFsegmentation is run and can be deleted once the samples are segmented.
+
+
+  __Mixing paired and unpaired samples__
 
 ''Performing BAFsegmentation''