Support for read groups:
Support ‘pool’ read groups taken from BED file, e.g.:
nCoV2019_1
nCoV2019_2
Do variant calling separately on each group, permits detection of incongruent mutations e.g. from contamination
Update to nanopolish 0.12.5 fo more informative VCF output
Change nanopore filtering to support new VCF output (e.g. strand-bias)
Support indels with bcftools consensus
Longshot added to Medaka to filter VCF on depth
New workflow model - all commands run "one per sample", script nanopolish index
Add 'artic gupplyplex' for support for demultiplexed Guppy output to replace 'artic gather'
Fix for align_trim to remove erroneous CIGAR strains that can cause medaka to fail
Support for amplicons v3 format file (Will Rowe)
Test suite (Will Rowe)
Documentation (Will Rowe)
Remove old deprecated code (Will Rowe)
Support for read groups: Support ‘pool’ read groups taken from BED file, e.g.: nCoV2019_1 nCoV2019_2 Do variant calling separately on each group, permits detection of incongruent mutations e.g. from contamination Update to nanopolish 0.12.5 fo more informative VCF output Change nanopore filtering to support new VCF output (e.g. strand-bias) Support indels with bcftools consensus Longshot added to Medaka to filter VCF on depth New workflow model - all commands run "one per sample", script nanopolish index Add 'artic gupplyplex' for support for demultiplexed Guppy output to replace 'artic gather' Fix for align_trim to remove erroneous CIGAR strains that can cause medaka to fail Support for amplicons v3 format file (Will Rowe) Test suite (Will Rowe) Documentation (Will Rowe) Remove old deprecated code (Will Rowe)