5.7 years ago by
As cwarden45 noted,
pindel2vcf is part of the pindel project and comes with it if you build it yourself from the pindel source package.
However WUSTL's pindel binary Debian package contains only
pindel0.2.4t and documentation, as you found, and there are no other pindel-related binary packages alongside it, which there might have been if the utilities had been split out of the main package.
So this is an error in packaging. When they made this package,
sam2pindel were mentioned only in INSTALL and not the Makefile, so it would have been easy to accidentally omit them. As of last week, they have been added to the Makefile. Hopefully WUSTL will update their pindel package to the current version and revisit the packaging scripts to include the associated utilities.
In the meantime, your alternative is to compile
sam2pindel from source yourself. This is relatively simple as they don't need any third-party libraries; e.g.,
pindel2vcf can be compiled just with
g++ -O3 pathtopindelsrcdir/src/vcfcreator.cpp -o pindel2vcf
and then you can copy
pindel2vcf to somewhere convenient in your
$PATH, perhaps $HOME/bin.