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• feature/bwa_mem2_update
• develop
• master
• no_samtools_view
• feature/read_install_config
• feature/dv_glnexus_logic
• feature/plink_fixes
• 1697/merge
• release/v9.0.5
• 1711/merge
• 1710/merge
• feature/vt_decompose_to_norm
• rm_path_2
• 1712/merge
• feature/conda_perl_install
• 1713/merge
• 1714/merge
• feature/vt_decompose_to_norm_expansionhunter
• update-codeowners
• 1715/merge
• feature/vt_uniq_to_norm_plink
• v9.0.5
• release/mip9.0.5
• 1716/merge
• 1717/merge
• feature/vt_decompose_to_norm_svcombinevariantcallsets
• 1718/merge
• feature/mip_container
• 1720/merge
• 1721/merge
• feature/setup_script_gpu
• feature/rm_mpileup
• 1723/merge
• feature/container_install
• 1724/merge
• feature/chanjo_docker
• 1725/merge
• feature/check_mip_executable
• 1726/merge
• feature/rm_check_future_filesystem_for_directory
• 1728/merge
• 1729/merge
• feature/rm_a_dir_from_tests
• feature/rm_delete_file
• 1730/merge
• feature/replace_mip_bind
• 1731/merge
• 1732/merge
• hotfix/slurm_jobids
• v9.0.6
• 1733/merge
• feature/check_vcfparser_cli
• 1734/merge
• release/v9.1.0
• 1736/merge
• 1741/merge
• feature/vcfparser_fix
• 1737/merge
• feature/star_options
• feature/carton
• 1742/merge
• v9.1.0
• 1743/merge
• feature/mip_executable
• 1744/merge
• feature/median_coverage
• 1745/merge
• feature/generate_contig_interval_file
• 1746/merge
• feature/build_docker
• 1747/merge
• feature/pre-commit
• feature/container_constants
• 1748/merge
• 1749/merge
• feature/doc
• 1750/merge
• feature/rm_module_version
• 1751/merge
• deeptrio_install
• release/9.1.1
• 1752/merge
• v9.1.1
• feature/rm_file_format_mip
• 1753/merge
• feature/deeptrio_install
• feature/varg_docker
• 1754/merge
• feature/slurm_mip
• 1756/merge
• feature/load_pli_file
• feature/bwakit
• 1758/merge
• feature/rm_strict
• 1759/merge
• 1755/merge
• 1760/merge
• feature/data_constraint
• feature/markduplicates_mem
• release/v9.1.2
• feature/create_vep_synonyms_file
• 1761/merge
• 1762/merge
• feature/loqusdb_headers
• 1763/merge
• 1764/merge
• feature/broad_aln
• feature/get_exome_target_bed_file
• 1765/merge
• feature/get_path_entries
• 1766/merge
• feature/get_gatk_intervals
• 1767/merge
• feature/set_merged_infile_prefix
• 1768/merge
• feature/parse_download_reference_parameter
• 1769/merge
• feature/get_merged_infile_prefix
• 1770/merge
• 1771/merge
• feature/set_conda_path
• 1772/merge
• feature/get_package_source_env_cmds
• 1773/merge
• feature/rtg_vcfeval_update
• 1774/merge
• get_recipe_resources
• 1775/merge
• 1776/merge
• feature/set_rankvariants_ar
• feature/set_container_bind_paths
• 1777/merge
• feature/set_programs_for_installation
• 1778/merge
• feature/set_recipe_bwa_mem
• 1779/merge
• feature/set_recipe_deepvariant
• 1780/merge
• feature/turn_off_deeptrio
• 1781/merge
• feature/update_dynamic_config_parameters
• 1783/merge
• v9.1.2
• feature/deeptrio_rollback
• 1784/merge
• 1782/merge
• feature/set_recipe_gatk_variantrecalibration
• 1785/merge
• feature/external_data
• 1789/merge
• feature/update_with_dynamic_config_parameters
• 1790/merge
• feature/set_recipe_on_analysis_type
• feature/set_recipe_star_aln
• 1791/merge
• feature/rna_markduplicates
• 1793/merge
• feature/set_io_files
• 1794/merge
• feature/get_io_files
• 1795/merge
• feature/parse_io_outfiles
• 1796/merge
• feature/rna_fixes
• 1797/merge
• 1798/merge
• release/v9.1.3
• feature/build_stream_file_cmd
• 1799/merge
• feature/get_sampling_fastq_files
• 1801/merge
• feature/gencode_bed_file
• 1802/merge
• feature/get_number_of_male_reads
• 1805/merge
• feature/update_gender_info
• 1807/merge
• 1808/merge
• feature/gres_update
• feature/dv_default_from_gpu_to_cpu
• 1809/merge
• 1810/merge
• feature/parse_fastq_for_gender
• delete-extra-docker-workflow
• 1811/merge
• feature/metric_deliverables
• 1812/merge
• v9.1.3
• feature/glnexus_mem_reqs
• 1813/merge
• feature/merge_v9.1.3
• 1814/merge
• feature/genbank_haplogroup
• 1815/merge
• 1816/merge
• feature/cleanup_gent-db
• feature/stranger_update
• 1817/merge
• feature/megafusion
• 1819/merge
• feature/rename_star_fusion_out
• 1820/merge
• feature/update_htslib
• feature/case_fusions
• 1822/merge
• 1821/merge
• feature/recipe_template
• 1823/merge
• feature/update_picard
• 1825/merge
• feature/rm_split_fastq_file
• 1826/merge
• feature/add_percentage_mapped_reads_from_samtool
• 1829/merge
• feature/serial_fusion_calling
• 1830/merge
• feature/update_tiddit
• 1831/merge
• feature/rename_arriba_contigs
• 1832/merge
• 1833/merge
• feature/update_sambamba
• 1835/merge
• feature/reference_check_vt
• docker_build_n_push_action
• 1836/merge
• feature/pdfmerger
• 1838/merge
• feature/generate_readable_commands
• feature/bwa-mem2
• 1839/merge
• feature/update_smncopynumbercaller
• 1840/merge
• feature/update_cyrius
• 1841/merge
• 1842/merge
• feature/deepvariant_housekeeper_integration
• 1843/merge
• 1844/merge
• feature/clinical_fusion_report
• feature/bcftools_norm_fix_reference
• 1845/merge
• feature/bwa-mem2_update
• feature/revert_generate_readable_commands
• 1847/merge
• feature/splice_junction_tracks
• 1848/merge
• 1849/merge
• feature/rename_quant_file
• feature/rna_resource_bump
• 1850/merge
• feature/splice_track_fix
• 1852/merge
• 1853/merge
• feature/sambamba_rollback
• 1854/merge
• 1855/merge
• feature/update_telomerecat
• feature/remove_vt_install
• 1856/merge
• 1857/merge
• feature/fix_gatk_combine_cli
• feature/update_svdb
• 1858/merge
• feature/update_gatk
• feature/rna_vcfparser
• 1860/merge
• 1861/merge
• feature/star_update
• 1862/merge
• 1863/merge
• feature/update_vep
• feature/deliverable_update
• 1864/merge
• feature/arriba_update
• 1865/merge
• feature/rna_genome_ref
• 1866/merge
• feature/megafusion_update
• 1867/merge
• feature/update_starfusion
• feature/update_reference
• 1868/merge
• 1869/merge
• feature/gencode_transcripts
• 1871/merge
• 1872/merge
• feature/bedtools
• feature/rna_doc
• 1873/merge
• feature/delly_update
• 1874/merge
• 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
• 1911/merge
• release/10.0.1
• feat/stranger_update
• 1915/merge
• v10.0.1
• 1916/merge
• feature/gnomad_3.1.1_download
• release/10.0.2
• 1918/merge
• 1919/merge
• feature/hmtnote
• feature/gnomad_mt
• 1920/merge
• v10.0.2
• 1922/merge
• 1921/merge
• release/10.0.3
• 1923/merge
• v10.0.3
• 1924/merge
• feature/set_resources
• 1925/merge
• feature/update_download_paths
• 1926/merge
• 1927/merge
• 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
• 1937/merge
• 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
• 1959/merge
• 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
• 1975/merge
• feature/gatk_for_mt
• release/10.2.4
• 1976/merge
• v10.2.4
• 1978/merge
• 1979/merge
• release/10.2.5
• v10.2.5
• 1980/merge
• v11.0.0
• 1984/merge
• 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
• 2024/merge
• 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
• 2032/merge
• 2033/merge
• exp_catalog
• 2034/merge
• 2035/merge
• v11.2.0
• release/11.2.1
• 2036/merge
• v11.2.1
• 2037/merge
• 2038/merge
• sv_updates
• 2039/merge
• release/11.2.2
• v11.2.2
• 2040/merge
• bump_retroseq_time
• 2041/merge
• 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

feat(bwa-mem2): update index names