Mauricio Carneiro
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5298e3a942
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Making the outputDir optional. Default = ./
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2011-07-05 16:30:41 -04:00 |
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Mauricio Carneiro
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7d3dfdfdf2
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Updating the MDCP to use the classpath for the GATK jar, removing -gatk parameter.
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2011-07-05 16:30:10 -04:00 |
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Mauricio Carneiro
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b0fb63e20a
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moving the example scala scripts to the qscripts package.
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2011-07-01 16:14:59 -04:00 |
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Mauricio Carneiro
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d19351f71a
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Added capability of running multiple bam files in the same directory.
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2011-07-01 16:02:28 -04:00 |
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Mauricio Carneiro
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197b7141c1
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Added an optional argument -bt <num_threads> for BWA to run multithreaded.
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2011-06-30 14:41:57 -04:00 |
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Mauricio Carneiro
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f4463d38ca
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BWA requires pair ended reads to be sorted by read names when operating over BAM files, but Picard sorts by coordinate, so in case we use BWA in pair ended reads, the pipeline now resorts the BAM in read name order, realigns it then sorts it in coordinate order.
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2011-06-30 14:29:21 -04:00 |
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Mauricio Carneiro
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efd99c3c11
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new home for the core qscripts
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2011-06-30 11:32:06 -04:00 |
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Mauricio Carneiro
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1085df8b7b
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Making the BQSR pipeline publicly available and supported.
this is for all the Pacbio validation that is going on right no in the cancer group. They are all using this script, and I'm happy to support it.
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2011-06-29 16:05:32 -04:00 |
David Roazen
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3c9497788e
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Reorganized the codebase beneath top-level public and private directories,
removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
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2011-06-28 06:55:19 -04:00 |