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


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Timestamp:
Jun 1, 2010, 3:34:12 PM (12 years ago)
Author:
markus
Comment:

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  • se.lu.onk.BAFsegmentation

    v35 v36  
    1010
    1111=== News ===
    12  
     12
     13 * Jun. 1, 2010. BAFsegmentation 1.2.0 release. Added support for paired tumor-normal samples.
     14
    1315 * 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.
    1416
     
    2426=== Future plans ===
    2527
    26  * Add support for using paired tumor-normal samples.
    2728 * Adaptation of BAFsegmentation to samples having 100% tumor content, for example, cell-lines.
    2829 * Integration of log R ratio into calling of regions and their type.
     
    3435=== Download BAFsegmentation ===
    3536
    36 [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).]
     37[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).]
    3738
    3839=== Supplemental Data ===
     
    7172 
    7273''Input data format''
     74 
     75  __Unpaired samples__
     76
    7377  BAFsegmentation is applied to data for a set of samples in a file that should be tab-delimited in the following format:
    7478  ||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||...||
     
    8488  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.
    8589
    86   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.
     90  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.
     91
     92  __Paired tumor-normal samples__
     93
     94  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:
     95  ||Name||Chr||Position||sample1.GType || sample1.B Allele Freq||sample1.Log R Ratio||sample2.GType||sample2.B Allele Freq||sample2.Log R Ratio||...||
     96  ||rs12354060||1||10004||AA||1||0.110391||AB||1||-0.05188531||...||
     97  ||rs2691310||1||46844||AB||0.5519782||0.2984372||BB||0.4636427||0.3640218||...||
     98  ||...||...||...||...||...||...||...||...||...||...||
     99
     100  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:
     101
     102  {{{ 
     103    perl split_samples.pl --data_file=example/example_beadstudio_paired_data.txt
     104  }}}
     105  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.
     106
     107  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.
     108
     109
     110  __Mixing paired and unpaired samples__
    87111
    88112''Performing BAFsegmentation''