# Tool Descriptions

| Tool                                                                                                                                               | Version         |
| -------------------------------------------------------------------------------------------------------------------------------------------------- | --------------- |
| [Fgbio GroupReadsByUmi](https://github.com/msk-access/cwl-commandlinetools/tree/develop/fgbio_group_reads_by_umi_1.2.0)                            | **1.2.0**       |
| [Fgbio CollectDuplexSeqMetrics](https://github.com/msk-access/cwl-commandlinetools/tree/develop/fgbio_collect_duplex_seq_metrics_1.2.0)            | **1.2.0**       |
| [Fgbio CallDuplexConsensusReads](https://github.com/msk-access/cwl-commandlinetools/tree/develop/fgbio_call_duplex_consensus_reads_1.2.0)          | **1.2.0**       |
| [GATK SamToFastq](https://github.com/msk-access/cwl-commandlinetools/tree/develop/gatk_sam_to_fastq_4.1.8.0)                                       | **4.1.8.0**     |
| [BWA mem](https://github.com/msk-access/cwl-commandlinetools/tree/develop/bwa_mem_0.7.17)                                                          | **0.7.17**      |
| [Picard AddOrReplaceReadGroups](https://github.com/msk-access/cwl-commandlinetools/tree/develop/picard_add_or_replace_read_groups_4.1.8.1)         | **4.1.8.1**     |
| [GATK MergeBamAlignment](https://github.com/msk-access/cwl-commandlinetools/tree/develop/gatk_merge_bam_alignment_4.1.8.0)                         | **4.1.8.0**     |
| [bedtools genomecov](https://github.com/msk-access/cwl-commandlinetools/tree/develop/bedtools_genomecov_v2.28.0_cv2)                               | **2.28.0\_cv2** |
| [bedtools merge](https://github.com/msk-access/cwl-commandlinetools/tree/develop/bedtools_merge_v2.28.0_cv2)                                       | **2.28.0\_cv2** |
| [ABRA2](https://github.com/msk-access/cwl-commandlinetools/tree/develop/abra2_2.22)                                                                | **2.22**        |
| [Picard FixMateInformation](https://github.com/msk-access/cwl-commandlinetools/tree/develop/picard_fix_mate_information_4.1.8.1)                   | **4.1.8.1**     |
| [Fgbio FilterConsensusReads](https://github.com/msk-access/cwl-commandlinetools/tree/develop/fgbio_filter_consensus_reads_1.2.0)                   | **1.2.0**       |
| [Fgbio Post-processing](https://github.com/msk-access/cwl-commandlinetools/tree/develop/fgbio_postprocessing_simplex_filter_0.1.8)                 | **0.1.8**       |
| [Picard CollectAlignmentSummaryMetrics](https://github.com/mskcc/cwl-commandlinetools/tree/develop/picard_collect_alignment_summary_metrics_2.8.1) | **2.8.1**       |
