If you love CRAC and you want to get the most out of it, take a look at the new version of the CracTools that is a complete toolbox designed to build pipelines (in Perl) on top of CRAC.

It is also shipped with a command-line tool that extracts splicing variants, chimeric variants, indels and SNPs identified by CRAC at the read level then collapses them into standard formats (BED,VCF).

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