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- abra2_2.22/README.md-21
- access_utils/0.1.1/general_stats_parse.cwl+16-34
- bedtools_genomecov_v2.28.0_cv2/README.md-56
- bedtools_merge_v2.28.0_cv2/README.md-57
- disambiguate_1.0.0/README.md-52
- docs/SUMMARY.md+71-73
- docs/abra2/README.md+2
- docs/abra2/abra2_2.17.md+15-14
- docs/abra2/abra2_2.22.md+21
- docs/bedtools/README.md+2
- docs/bedtools/bedtools_genomecov_v2.28.0_cv2.md+43
- docs/bedtools/bedtools_merge_v2.28.0_cv2.md+43
- docs/disambiguate/README.md+2
- docs/disambiguate/disambiguate_1.0.0.md+53
- docs/fgbio/README.md+2
- docs/fgbio/fgbio_call_duplex_consensus_reads_1.2.0.md+8-8
- docs/fgbio/fgbio_collect_duplex_seq_metrics_1.2.0.md+8-7
- docs/fgbio/fgbio_fastq_to_bam_1.2.0.md+8-8
- docs/fgbio/fgbio_filter_consensus_reads_1.2.0.md+8-8
- docs/fgbio/fgbio_group_reads_by_umi_1.2.0.md+8-8
- docs/fgbio/fgbio_postprocessing_simplex_filter_0.1.8.md+8-7
- docs/gatk/README.md+2
- docs/gatk/gatk_apply_bqsr_4.1.8.1.md+43
- docs/gatk/gatk_applybqsr_4.1.2.0.md+43
- docs/gatk/gatk_base_recalibrator_4.1.8.1.md+43
- docs/gatk/gatk_baserecalibrator_4.1.2.0.md+43
- docs/gatk/gatk_merge_bam_alignment_4.1.8.0.md+8-8
- docs/gatk/gatk_merge_sam_files_4.1.8.0.md+8-8
- docs/gatk/samtofastq-v4.1.8.0.md+2
- docs/manta/README.md+2
- docs/manta/manta_1.5.1.md+14-13
- docs/marianas/README.md+2
- docs/marianas/marianas_collapsing_first_pass_1.8.1.md+19
- docs/marianas/marianas_collapsing_second_pass_1.8.1.md+19
- docs/marianas/marianas_process_loop_umi_1.8.1.md+19
- docs/marianas/marianas_separate_bams_1.8.1.md+33
- docs/merge-fastq/README.md+2
- docs/merge-fastq/merge_fastq_0.1.7.md+11-11
- docs/mutect/README.md+2
- docs/mutect/mutect_1.1.5.md+12-13
- docs/picard-tools/README.md+2
- docs/picard-tools/picard_add_or_replace_read_groups_1.96.md+12-12
- docs/picard-tools/picard_add_or_replace_read_groups_2.21.2.md+8-9
- docs/picard-tools/picard_add_or_replace_read_groups_4.1.8.1.md+8-9
- docs/picard-tools/picard_collect_alignment_summary_metrics_2.21.2.md+8-8
- docs/picard-tools/picard_collect_alignment_summary_metrics_2.8.1.md+11-11
- docs/picard-tools/picard_collectmultiplemetric_2.21.2.md+8-8
- docs/picard-tools/picard_collectmultiplemetric_2.8.1.md+11-11
- docs/picard-tools/picard_fix_mate_information_1.96.md+15-14
- docs/picard-tools/picard_fix_mate_information_2.21.2.md+10-10
- docs/picard-tools/picard_fix_mate_information_4.1.8.1.md+10-10
- docs/picard-tools/picard_hsmetrics_2.21.2.md+8-9
- docs/picard-tools/picard_hsmetrics_2.8.1.md+26
- docs/picard-tools/picard_mark_duplicates_1.96.md+20
- docs/picard-tools/picard_mark_duplicates_2.21.2.md+8-8
- docs/picard-tools/picard_mark_duplicates_2.8.1.md+20
- docs/picard-tools/picard_mark_duplicates_4.1.8.1.md+8-8
- docs/trim-galore/README.md+2
- docs/trim-galore/trim_galore_0.6.2.md+15-14
- docs/ubuntu-utilites/README.md+2
- docs/ubuntu-utilites/utilities_ubuntu_18.04.md+26
- docs/waltz/README.md+2
- docs/waltz/waltz_count_reads_3.1.1.md+12-10
- docs/waltz/waltz_pileupmatrices_3.1.1.md+12-10
- gatk_ApplyBQSR_4.1.2.0/README.md-128
- gatk_BaseRecalibrator_4.1.2.0/README.md-142
- gatk_apply_bqsr_4.1.8.1/README.md-128
- gatk_base_recalibrator_4.1.8.1/README.md-142
- marianas_collapsing_first_pass_1.8.1/README.md-19
- marianas_collapsing_second_pass_1.8.1/README.md-19
- marianas_process_loop_umi_1.8.1/README.md-19
- marianas_separate_bams_1.8.1/README.md-33
- multiqc/1.10.1.7/multiqc.cwl+12-2
- picard_hsmetrics_2.8.1/README.md-26
- picard_mark_duplicates_1.96/README.md-20
- picard_mark_duplicates_2.8.1/README.md-20
- utilities_ubuntu_18.04/README.md-25
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