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Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
SystemVerilog C++ Perl Python Makefile Shell C
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demo add reference index
gmt-web 0.2.4 -> 0.2.5
gmt start porting config over to new gmt site
somatic_filter not so good fisher exact test implementation
src remove one bug in -c region and turn off inter-chr in default setting
.gitignore added .gitignore 2012 mar 29, add Keiran's new and to trunk.
COPYING.txt * Added copy of the GPLv3 license
INSTALL new vcfcreator for tcga
Makefile makefile again Convert README to markdown
README_INSTALL added install instruction on htslib
RELEASE increased maximum runtime for test 2012 mar 29, add Keiran's new and to trunk.
gmt.yml fix config typo



To compile Pindel you need GNU Make, GCC and cppcheck and python. Usually they are already installed on Linux. On the Mac you will need to install XCode (3 or higher), the latest version can be downloaded from the Mac App Store. cppcheck can be installed with Fink, MacPorts or Homebrew, where homebrew is more convenient if you don't need to install other software from source.

Pindel requires samtools; you can download the latest version of samtools from the Samtools Sourceforge site. You need to extract and build samtools before you compile Pindel. Refer to the documentation of samtools for the requirements to build samtools.

If you make the Pindel project the first time, it will create a Makefile.local. It will try to be smart and generate this file with the correct location of samtools if you specify it on the make commandline.

make SAMTOOLS=~/samtools-0.1.18

The Makefile.local also includes a couple of options for the different tests. The *_TIME options define the max execution time for the jobs in the acceptance tests, if they are exceeded the acceptance tests will fail.

The THREADS option defines the number of threads used in the functional tests, this should be at least 2, it is recommended to match the number of cores in your system to get the fastest execution time.

Different tests

The following test targets are defined:

  1. acceptance-tests
  2. coverage-tests
  3. functional-tests
  4. regression-tests
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