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• feature/get_gatk_intervals
• develop
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• no_samtools_view
• feature/read_install_config
• feature/bwa_mem2_update
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• feature/plink_fixes
• 1697/merge
• release/v9.0.5
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• v9.0.5
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• v9.0.6
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• feature/vcfparser_fix
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• feature/star_options
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• v9.1.0
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• feature/median_coverage
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• feature/generate_contig_interval_file
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• release/9.1.1
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• release/v9.1.2
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• feature/get_merged_infile_prefix
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• get_recipe_resources
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• feature/set_programs_for_installation
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• feature/set_recipe_bwa_mem
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• feature/update_dynamic_config_parameters
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• v9.1.2
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• feature/set_recipe_gatk_variantrecalibration
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• feature/external_data
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• feature/update_with_dynamic_config_parameters
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• feature/set_recipe_on_analysis_type
• feature/set_recipe_star_aln
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• feature/rna_markduplicates
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• feature/set_io_files
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• feature/get_io_files
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• feature/parse_io_outfiles
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• feature/rna_fixes
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• release/v9.1.3
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• feature/get_sampling_fastq_files
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• feature/gencode_bed_file
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• feature/get_number_of_male_reads
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• feature/update_gender_info
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• feature/gres_update
• feature/dv_default_from_gpu_to_cpu
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• feature/parse_fastq_for_gender
• delete-extra-docker-workflow
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• feature/metric_deliverables
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• v9.1.3
• feature/glnexus_mem_reqs
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• feature/merge_v9.1.3
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• feature/genbank_haplogroup
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• feature/cleanup_gent-db
• feature/stranger_update
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• feature/megafusion
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• feature/rename_star_fusion_out
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• feature/update_htslib
• feature/case_fusions
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• feature/recipe_template
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• feature/update_picard
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• feature/rm_split_fastq_file
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• feature/add_percentage_mapped_reads_from_samtool
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• feature/serial_fusion_calling
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• feature/update_tiddit
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• feature/rename_arriba_contigs
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• feature/update_sambamba
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• feature/reference_check_vt
• docker_build_n_push_action
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• feature/pdfmerger
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• feature/generate_readable_commands
• feature/bwa-mem2
• 1839/merge
• feature/update_smncopynumbercaller
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• feature/update_cyrius
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• feature/deepvariant_housekeeper_integration
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• feature/clinical_fusion_report
• feature/bcftools_norm_fix_reference
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• feature/bwa-mem2_update
• feature/revert_generate_readable_commands
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• feature/splice_junction_tracks
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• feature/rename_quant_file
• feature/rna_resource_bump
• 1850/merge
• feature/splice_track_fix
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• feature/sambamba_rollback
• 1854/merge
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• feature/update_telomerecat
• feature/remove_vt_install
• 1856/merge
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• feature/fix_gatk_combine_cli
• feature/update_svdb
• 1858/merge
• feature/update_gatk
• feature/rna_vcfparser
• 1860/merge
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• feature/star_update
• 1862/merge
• 1863/merge
• feature/update_vep
• feature/deliverable_update
• 1864/merge
• feature/arriba_update
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• feature/rna_genome_ref
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• feature/megafusion_update
• 1867/merge
• feature/update_starfusion
• feature/update_reference
• 1868/merge
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• feature/gencode_transcripts
• 1871/merge
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• feature/bedtools
• feature/rna_doc
• 1873/merge
• feature/delly_update
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• feature/glnexus
• 1875/merge
• 1876/merge
• feature/htslib
• feature/multiqc
• 1877/merge
• feature/bcftools_norm_cov
• 1878/merge
• feature/preseq
• 1879/merge
• 1880/merge
• feature/rseqc
• feature/rtg-tools
• 1881/merge
• 1882/merge
• feature/salmon
• feature/upd
• 1883/merge
• feature/update_rna_template
• 1884/merge
• 1885/merge
• feature/chromograph
• 1886/merge
• feature/blobfish
• 1887/merge
• feature/rseqc_build
• 1888/merge
• feature/bcftools_norm_update
• 1890/merge
• feature/rna_qc_mestrics
• 1891/merge
• feature/clinvar_ref
• 1892/merge
• release/10.0.0
• 1893/merge
• feature/fix_deepvariant_version_typo
• 1894/merge
• feature/no_atomize
• 1895/merge
• feature/bcftools_norm_recipe
• 1896/merge
• 1898/merge
• feature/info_download
• 1899/merge
• feature/rna_mt_contig
• feature/norm_rna_and_mt
• 1900/merge
• feature/recipe_bind_path_mod
• 1901/merge
• feature/norm_glnexus
• 1902/merge
• 1903/merge
• feature/rollback_telomercat
• feature/vcfparser_recipe_fix
• 1907/merge
• feature/cadd_index
• 1908/merge
• feature/htslib_rollback
• 1909/merge
• 1910/merge
• feature/bcftools_base
• v10.0.0
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• release/10.0.1
• feat/stranger_update
• 1915/merge
• v10.0.1
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• feature/gnomad_3.1.1_download
• release/10.0.2
• 1918/merge
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• feature/hmtnote
• feature/gnomad_mt
• 1920/merge
• v10.0.2
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• release/10.0.3
• 1923/merge
• v10.0.3
• 1924/merge
• feature/set_resources
• 1925/merge
• feature/update_download_paths
• 1926/merge
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• feature/qc_collect_deliverable
• feature/start_after_recipe
• 1929/merge
• feature/start_after_recipe_flag
• 1930/merge
• feature/gnu_awk
• 1931/merge
• v10.1.0
• v10.2.0
• 1932/merge
• feature/mitodel
• 1933/merge
• feature/found_in_tag
• 1936/merge
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• feature/deactivate_gatk
• update_software
• 1939/merge
• feature/limit_qc
• 1940/merge
• 1941/merge
• feature/ghcr_uri
• feature/update_glnexus_uri
• 1942/merge
• 1943/merge
• feat/fix_glnexus_permission
• 1946/merge
• hmtnote/quickfix
• hotfix/mt_filter
• 1947/merge
• feature/local_images
• 1950/merge
• v10.2.1
• 1952/merge
• feature/sv_freq_filter
• 1953/merge
• 1949/merge
• feature/references
• 1955/merge
• feature/hmtnote_version_regex
• feature/fixing_loqus_headers
• 1956/merge
• feature/trim_mt_anno_whitespace
• 1957/merge
• feature/change_to_bcftools_concat
• 1958/merge
• hotfix/add_missing_qc_value
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• v10.2.2
• 1960/merge
• 1962/merge
• feature/more_qc_metrics
• 1964/merge
• feature/increased_AF_cutoff
• 1965/merge
• feature/paper_and_redirection
• feature/fixing_test_coverage
• 1966/merge
• release/11.0.0
• 1967/merge
• feature/gens
• gens
• 1972/merge
• feature/gens_install
• 1973/merge
• release/10.2.3
• 1974/merge
• v10.2.3
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• feature/gatk_for_mt
• release/10.2.4
• 1976/merge
• v10.2.4
• 1978/merge
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• release/10.2.5
• v10.2.5
• 1980/merge
• v11.0.0
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• release/11.0.1
• 1985/merge
• v11.0.1
• 1986/merge
• upd_on_unaffected_children
• 1989/merge
• expansionhunter_5
• 1990/merge
• 1991/merge
• svdb_update
• feature/gens_preproc_container_fix
• 1992/merge
• 1993/merge
• feature/gens_preproc_version_1.0.2
• updating_programs
• 1996/merge
• update_databases
• 1998/merge
• fixes_before_mip11.1
• 1999/merge
• mip11.0.2
• 2000/merge
• v11.0.2
• 2001/merge
• 2002/merge
• release/mip11.1
• release/11.0.3
• 2003/merge
• v11.0.3
• 2004/merge
• v11.1.0
• 2005/merge
• release/11.1.1
• 2006/merge
• v11.1.1
• 2007/merge
• tiddit_update
• 2008/merge
• 2009/merge
• exphun_catalog_update
• salmon_memory
• 2010/merge
• 2011/merge
• bump_rna_mergesamfiles_mem
• 2012/merge
• update_megafusion
• 2013/merge
• remove_rseqc_read_duplication
• release/11.2.0
• 2014/merge
• release/11.1.2
• 2017/merge
• v11.1.2
• feature/fixing_gens_index
• 2018/merge
• 2019/merge
• release/11.1.3
• 2020/merge
• v11.1.3
• 2022/merge
• retroseq_recipe
• 2023/merge
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• me_merge_vcf
• 2025/merge
• annotate_me
• 2026/merge
• vep_me
• 2028/merge
• vep_me_2
• 2029/merge
• 2030/merge
• remove_exon_anno
• me_filter
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• exp_catalog
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• v11.2.0
• release/11.2.1
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• v11.2.1
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• sv_updates
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• release/11.2.2
• v11.2.2
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• bump_retroseq_time
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• clinvar_update
• 2042/merge
• release/12.0.0
• 2043/merge
• v12.0.0
• 2048/merge
• 2050/merge
• update_codeowners
• vcf_rerun
• annotate-clinvar-dataset
• improper_pair_eval

Update lib/MIP/Gatk.pm