Release v1.1.0

Updates to the sentieon-cli pipelines

General updates

• Improved logging
• Add a Dockerfile

DNAscope LongRead

• Incorporate mosdepth for alignment QC
• Add haploid gVCF output

Release v1.0.0

Support installation with pip using sdist packages.

Release v0.3.0

Adds a DNAscope pipeline for short-read data

Features of the DNAscope pipeline:

• A single command for alignment, pre-processing and metrics collection, SNV/indel and SV calling
• Supports input read data in FASTQ, uBAM, uCRAM, BAM, or CRAM formats
• Uses MultiQC to aggregate multiple metrics files into a single report

Release v0.2.0

Updates to the DNAscope LongRead pipeline

New Features

• Supports one or more unaligned input files in fastq/uBAM/uCRAM formats.
• Supports one or more aligned input in BAM/CRAM formats. The aligned data can be re-aligned using the --align flag. Regroups (and other tags including methylation) will be retained from the input file.
• Alignment of ONT or HiFi reads using minimap2 with output alignments in the BAM or CRAM formats.
• Haploid variant calling.
• Structural variant calling with LongReadSV.

Release v0.1.0

Initial release of the sentieon-cli tool, supporting germline variant calling with the DNAscope LongRead pipeline.