v1.2a

Added support for cram format

• ext parameter added to specify format
• default is now cram

v1.2

New features:
• rename option --tn_pairs to --input_file (because it now also works for germline mode)
• add option to provide sample name to be used in VCF naming (triggered when sample column is detected in input_file)
• add option to provide vcf to perform genotyping (triggered when vcf column is detected in input_file)
Debug:
• add INFO field for AF and COV to VCF to avoid crashes for downstream analyses with bcftools when using AF option

v1.1

• Added dockerfile and singularity containers
• circleci tests
• debug AF option
• add (beta) genotyping option

v1.0

Initial release