v3.6.2

Fixed issue with temp directory in bcftools.

v3.6.1

Added option to disable region-based coverage normalization for high coverage samples. Fixed installation and package import bugs.

v3.6.0

CSI indices generated for VCF files instead of TBI to accommodate larger contigs.

v3.5.0

CRAM files are supported in input as well as in phased output if whatshap version>=2 is being used with NanoCaller.

v3.4.1

Fixed a critical bug in haploid mode introduced in v3.3.0.

v3.4.0 Allelic Depth

VCF files contain total and strand-specific allele depths for SNP calls from SNP calling models. A new mode for short ONT reads (5-10kbp) added. --phase_qual_score parameter filters out low quality SNP calls from phasing by WhatsHap; these SNP calls are kept in the output, but neither phased nor used for phasing reads.

v3.3.0

Detailed description of SNP calls, including unfiltered SNP calls for variants determined to be false by NanoCaller, and inclusion of per-base probability output. Quality score has been adjusted to be on Phred scale.

v3.2.0 Haploid Variant Calling

Support added for haploid variant calling which has significant improvement in recall for indel calling. New feature generation methods and models are are used for haploid SNP and indel calling. Now chrY and chrM are assumed to be haploid, with additional parameter --haploid_X to specify if chrX is haploid. Another parameter --haploid_genome can be used for haploid variant calling on all chromosomes.

v3.1.0

Fixed several indel calling bugs, including allele sequence prediction and normalization, with allele normalization step reverted to rtg-tools.

v3.0.1

Several critical bugs regarding coverage normalization and integer overflow fixed.