ngs convert

Overview

The ngs convert subcommand converts between various next-generation sequencing files formats.

Conversions between the following file formats are supported or are scheduled to be supported in the near future.

From	To	Supported	(Predicted) Version Support Included
SAM	BAM	✅	Released in v0.4.0
BAM	SAM	✅	Released in v0.4.0
SAM	CRAM	✅	Released in v0.4.0
CRAM	SAM	✅	Released in v0.4.0
BAM	CRAM	✅	Released in v0.4.0
CRAM	BAM	✅	Released in v0.4.0

From	To	Supported	(Predicted) Version Support Included
GFF	Block-gzipped GFF	✅	Released in v0.4.0

Subcommands
- ngs convert
- ngs derive
- ngs generate
- ngs index
- ngs list
- ngs plot
- ngs qc
  - Record-based Facets
  - Sequence-based Facets
    - Coverage metrics
    - Edit metrics
- ngs view
Development
- Common arguments