Highlights
Added
- Added SV and CNV annotation, ranking and filtering
- Added Severus as the default SV caller
- Added longphase as the default phaser
- Added vcfstatsreport from DeepVariant for SNVs
Changed
- Moved documentation to https://genomic-medicine-sweden.github.io/nallo/
- Updated hifiasm with new default parameters for telomeres and scaffolding
- Changed SV (and CNV) merging strategies to use SVDB per family
- Changed output structure
Removed
- Removed unnecessary BAM to Fastq conversions and concatenations
- Removed support for co-phasing SNVs and SVs with HiPhase, as the officially supported caller (pbsv) is not in the pipeline
- Removed support for automatically creating an echvar database with SNVs and INDELs
Fixed
- Fixed unsorted variants in SNV outputs (#362)
- Fixed
--vep_cachenot working as expected with tar.gz cache downloaded from VEP - Fixed minimap2 preset for ONT data being overwritten to
map-ontwhen it should have beenlr:hq, due to different settings in index and alignment processes (#392) - Fixed double sample names in HiFiCNV output
- Fixed missing/malformed software versions in
ADD_FOUND_IN_TAG,ADD_MOST_SEVERE_CSQ,ADD_MOST_SEVERE_PLI,SAMPLESHEET_PED,SOMALIER_PEDandTRGT - Fixed genmod assigning wrong models on chromosome X when named
chrX(#343) - Fixed genmod only scoring compounds in one family (#501)
Parameters
| Old parameter | New parameter |
|---|---|
--skip_aligned_read_qc |
--skip_qc |
--skip_raw_read_qc |
--skip_qc |
--sv_caller |
|
--minimap2_read_mapping_preset |
|
--genome |
|
--igenomes_ignore |
|
--max_cpus |
|
--max_memory |
|
--max_time |
|
--validationShowHiddenParams |
|
--validationSkipDuplicateCheck |
|
--validationS3PathCheck |
|
--monochromeLogs |
--monochrome_logs |
--filter_variants_hgnc_ids |
|
--filter_snvs_expression |
|
--filter_svs_expression |
|
--skip_short_variant_calling |
--skip_snv_calling |
--skip_assembly_wf |
--skip_genome_assembly |
--skip_mapping_wf |
--skip_alignment |
--skip_methylation_wf |
--skip_methylation_pileups |
--skip_phasing_wf |
--skip_phasing |
--variant_caller |
--snv_caller |
--parallel_snv |
--snv_calling_processes |
--cadd_prescored |
--cadd_prescored_indels |
--snp_db |
--echtvar_snv_databases |
--variant_catalog |
--stranger_repeat_catalog |
--bed |
--target_regions |
--hificnv_xy |
--hificnv_expected_xy_cn |
--hificnv_xx |
--hificnv_expected_xx_cn |
--hificnv_exclude |
--hificnv_excluded_regions |
--reduced_penetrance |
--genmod_reduced_penetrance |
--score_config_snv |
--genmod_score_config_snvs |
--score_config_sv |
--genmod_score_config_svs |
--parallel_alignments |
--alignment_processes |
--svdb_dbs |
--svdb_sv_databases |
Note
Parameter has been updated if both old and new parameter information is present.
Parameter has been added if just the new parameter information is present.
Parameter has been removed if new parameter information isn't present.
Module updates
| Tool | Old version | New version |
|---|---|---|
| fqcrs | 0.1.0 | |
| severus | 1.1 | |
| longphase | 1.7.3 | |
| genmod | 3.8.2 | 3.9 |
| WhatsHap | 2.2 | 2.3 |
| SVDB | 2.8.2 | |
| hifiasm | 0.19.8 | 0.20.0 |
| HiFiCNV | 0.1.7 | 1.0.0 |
| samtools/faidx | 1.2 | 1.21 |
| samtools/index | 1.2 | 1.21 |
| samtools/merge | 1.2 | 1.21 |
| stranger | 0.9.1 | 0.9.2 |
| multiqc | 1.21 | 1.25.1 |
| ensemblvep/filter_vep | 113 | |
| TRGT | 0.4.0 | 1.2.0 |
| bcftools/merge | 1.2 |
Note
Version has been updated if both old and new version information is present.
Version has been added if just the new version information is present.
Version has been removed if new version information isn't present.
Full Changelog: 0.3.2...0.4.0