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(How_to)_Call_somatic_SNVs_and_indels_using_MuTect2.md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
(How_to)_Create_a_snippet_of_reads_corresponding_to_a_genomic_interval.md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
(How_to)_Fix_a_badly_formatted_BAM.md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
(How_to)_Generate_an_unmapped_BAM_from_FASTQ_or_aligned_BAM.md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
(How_to)_Map_and_clean_up_short_read_sequence_data_efficiently.md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
(How_to)_Map_reads_to_a_reference_with_alternate_contigs_like_GRCh38.md
(How_to)_Mark_duplicates_with_MarkDuplicates_or_MarkDuplicatesWithMateCigar.md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
(How_to)_Simulate_reads_using_a_reference_genome_ALT_contig.md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
(howto)_Apply_hard_filters_to_a_call_set.md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
(howto)_Call_variants_with_HaplotypeCaller.md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
(howto)_Call_variants_with_the_UnifiedGenotyper.md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
(howto)_Discover_variants_with_GATK_-_A_GATK_Workshop_Tutorial.md
(howto)_Evaluate_a_callset_with_CollectVariantCallingMetrics.md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
(howto)_Evaluate_a_callset_with_VariantEval.md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
(howto)_Generate_a_"bamout_file"_showing_how_HaplotypeCaller_has_remapped_sequence_reads.md
(howto)_Get_started_with_GATK4_beta.md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
(howto)_Install_all_software_packages_required_to_follow_the_GATK_Best_Practices..md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
(howto)_Install_software_for_GATK_workshops.md
(howto)_Perform_local_realignment_around_indels.md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
(howto)_Recalibrate_base_quality_scores_=_run_BQSR.md
(howto)_Recalibrate_variant_quality_scores_=_run_VQSR.md
(howto)_Revert_a_BAM_file_to_FastQ_format.md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
(howto)_Run_Queue_for_the_first_time.md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
(howto)_Run_a_WDL_script_via_Cromwell_on_a_local_machine_(e.g._your_laptop).md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
(howto)_Run_the_GATK_for_the_first_time.md
(howto)_Run_the_genotype_refinement_workflow.md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
(howto)_Test_your_GATK_installation.md
(howto)_Test_your_Queue_installation.md
(howto)_Visualize_an_alignment_with_IGV.md
Appendix_to_(howto)_Discover_variants_with_GATK.md Archive of pre-GATK4 docs + Blog 2012 to 2019 Jan 6, 2020
Tutorial_files_provenance:_ASHG15.md
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