Thanks for the major update of the Freebayes wrapper, excellent! I've run into two issues, however. 1) When using "set allelic scope" I get the following error: Fatal error: Exit code 1 () freebayes: unrecognized option `--min-repeat-length' did you mean --min-repeat-size ? 2) When using a vcf file as input I get the following error: Fatal error: Exit code 1 () open: No such file or directory [bgzf_check_bgzf] failed to open the file: input_variant_vcf.vcf.gz [tabix++] was bgzip used to compress this file? input_variant_vcf.vcf.gz I'd be happy to help resolve these. Is there a bitbucket repo somewhere to submit pull requests? Also, I'm not sure if this is best sent to this list or put into Trello, etc. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University