# Inputs Description

{% hint style="warning" %}
Common workflow language execution engines accept two types of input that are [JSON](https://json.org) or [YAML](https://yaml.org), please make sure to use one of these while generating the input file. For more information refer to: <http://www.commonwl.org/user_guide/yaml/>
{% endhint %}

## **Parameter Used by Tools**

### Common Parameters Across Tools

|      **Argument Name**     |                                                                                                                     Summary                                                                                                                    | Default Value |
| :------------------------: | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | :-----------: |
|   **reference\_sequence**  |                                  Reference sequence file. Please include ".fai", "^.dict", ".amb" , ".sa", ".bwt", ".pac" as secondary files if they are not present in the same location as the ".fasta" file                                 |               |
| **validation\_stringency** | GATK: Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. |               |
|   **create\_bam\_index**   |                                                                                                   GATK: Generate BAM index file when possible                                                                                                  |               |
|       **sort\_order**      |                                                                                           GATK: The order in which the merged reads should be output.                                                                                          |               |

### Fgbio [GroupReadsByUmi](https://github.com/msk-access/cwl-commandlinetools/tree/develop/fgbio_group_reads_by_umi_1.2.0)

|                     **Argument Name**                     |                                                                                       Summary                                                                                      | Default Value |
| :-------------------------------------------------------: | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | :-----------: |
|          **fgbio\_group\_reads\_by\_umi\_input**          |                                                                                 The input BAM file                                                                                 |               |
|         **fgbio\_group\_reads\_by\_umi\_strategy**        |                                                          The UMI assignment strategy. (identity, edit, adjacency, paired)                                                          |               |
|         **fgbio\_group\_reads\_by\_umi\_raw\_tag**        |                                                                           The tag containing the raw UMI.                                                                          |       RX      |
|    **fgbio\_group\_reads\_by\_umi\_output\_file\_name**   |                                                                              The output BAM file name                                                                              |               |
|     **fgbio\_group\_reads\_by\_umi\_min\_umi\_length**    | The minimum UMI length. If not specified then all UMIs must have the same length, otherwise, discard reads with UMIs shorter than this length and allow for differing UMI lengths. |               |
| **fgbio\_group\_reads\_by\_umi\_include\_non\_pf\_reads** |                                                                                Include non-PF reads.                                                                               |     False     |
| **fgbio\_group\_reads\_by\_umi\_family\_size\_histogram** |                                                                     Optional output of tag family size counts.                                                                     |               |
|          **fgbio\_group\_reads\_by\_umi\_edits**          |                                                                     The allowable number of edits between UMIs.                                                                    |       1       |
|       **fgbio\_group\_reads\_by\_umi\_assign\_tag**       |                                                                          The output tag for UMI grouping.                                                                          |       MI      |

### Fgbio [CollectDuplexSeqMetrics](https://github.com/msk-access/cwl-commandlinetools/tree/develop/fgbio_collect_duplex_seq_metrics_1.2.0)

|                         Argument Name                         |                                           Summary                                          | Default Value |
| :-----------------------------------------------------------: | :----------------------------------------------------------------------------------------: | :-----------: |
|      **fgbio\_collect\_duplex\_seq\_metrics\_intervals**      |                 Optional set of intervals over which to restrict analysis.                 |               |
|    **fgbio\_collect\_duplex\_seq\_metrics\_output\_prefix**   |                              Prefix of output files to write.                              |               |
|    **fgbio\_collect\_duplex\_seq\_metrics\_min\_ba\_reads**   |                      Minimum BA reads to call a tag family a ‘duplex’.                     |               |
|    **fgbio\_collect\_duplex\_seq\_metrics\_min\_ab\_reads**   |                      Minimum AB reads to call a tag family a ‘duplex’.                     |               |
|       **fgbio\_collect\_duplex\_seq\_metrics\_mi\_tag**       |                              The output tag for UMI grouping.                              |       MI      |
| **fgbio\_collect\_duplex\_seq\_metrics\_duplex\_umi\_counts** | If true, produce the .duplex\_umi\_counts.txt file with counts of duplex UMI observations. |               |
|     **fgbio\_collect\_duplex\_seq\_metrics\_description**     |          Description of data set used to label plots. Defaults to sample/library.          |               |

### Fgbio [CallDuplexConsensusReads](https://github.com/msk-access/cwl-commandlinetools/tree/develop/fgbio_call_duplex_consensus_reads_1.2.0)

|                             Argument Name                            |                                                                                                Summary                                                                                               | Default Value |
| :------------------------------------------------------------------: | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | :-----------: |
|            **fgbio\_call\_duplex\_consensus\_reads\_trim**           |                                                                 If true, quality trim input reads in addition to masking low Q bases.                                                                |               |
|        **fgbio\_call\_duplex\_consensus\_reads\_sort\_order**        |                                                                  The sort order of the output, if :none: then the same as the input.                                                                 |               |
|     **fgbio\_call\_duplex\_consensus\_reads\_read\_name\_prefix**    |                                                                                  The prefix all consensus read names                                                                                 |               |
|      **fgbio\_call\_duplex\_consensus\_reads\_read\_group\_id**      |                                                                          The new read group ID for all the consensus reads.                                                                          |               |
|     **fgbio\_call\_duplex\_consensus\_reads\_output\_file\_name**    |                                                                           Output SAM or BAM file to write consensus reads.                                                                           |               |
|         **fgbio\_call\_duplex\_consensus\_reads\_min\_reads**        |                                                                        The minimum number of input reads to a consensus read.                                                                        |               |
| **fgbio\_call\_duplex\_consensus\_reads\_min\_input\_base\_quality** |                                                                        Ignore bases in raw reads that have Q below this value.                                                                       |               |
|  **fgbio\_call\_duplex\_consensus\_reads\_max\_reads\_per\_strand**  | The maximum number of reads to use when building a single-strand consensus. If more than this many reads are present in a tag family, the family is randomly downsampled to exactly max-reads reads. |               |
|   **fgbio\_call\_duplex\_consensus\_reads\_error\_rate\_pre\_umi**   |                                                             The Phred-scaled error rate for an error prior to the UMIs being integrated.                                                             |               |
|   **fgbio\_call\_duplex\_consensus\_reads\_error\_rate\_post\_umi**  |                                                             The Phred-scaled error rate for an error post the UMIs have been integrated.                                                             |               |

### GATK [SamToFastq](https://github.com/msk-access/cwl-commandlinetools/tree/develop/gatk_sam_to_fastq_4.1.8.0)

|                        Argument Name                        |                                                                                                                 Summary                                                                                                                | Default Value |
| :---------------------------------------------------------: | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | :-----------: |
|       **gatk\_sam\_to\_fastq\_output\_name\_unpaired**      |                                                                                                     unpaired fastq output file name                                                                                                    |               |
|          **gatk\_sam\_to\_fastq\_output\_name\_R1**         |                                                                                                     Read1 fastq.gz output file name                                                                                                    |               |
|          **gatk\_sam\_to\_fastq\_output\_name\_R2**         |                                                                                                     Read2 fastq.gz output file name                                                                                                    |               |
| **gatk\_sam\_to\_fastq\_include\_non\_primary\_alignments** | If true, include non-primary alignments in the output. Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments. |               |
|      **gatk\_sam\_to\_fastq\_include\_non\_pf\_reads**      |              Include non-PF reads from the SAM file into the output FASTQ files. PF means 'passes filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads. See GATK Dictionary for more info.              |               |

### [BWA MEM](https://github.com/msk-access/cwl-commandlinetools/tree/develop/bwa_mem_0.7.17)

|         Argument Name        |                                                       Summary                                                      | Default Value |
| :--------------------------: | :----------------------------------------------------------------------------------------------------------------: | :-----------: |
|        **bwa\_mem\_Y**       |                  Force soft-clipping rather than default hard-clipping of supplementary alignments                 |               |
|        **bwa\_mem\_T**       |                 Don’t output alignment with score lower than INT. This option only affects output.                 |               |
|        **bwa\_mem\_P**       | In the paired-end mode, perform SW to rescue missing hits only but do not try to find hits that fit a proper pair. |               |
|     **bwa\_mem\_output**     |                                                Output SAM file name                                                |               |
|        **bwa\_mem\_M**       |                                        Mark shorter split hits as secondary                                        |               |
|        **bwa\_mem\_K**       |                     to achieve deterministic alignment results (Note: this is a hidden option)                     |               |
| **bwa\_number\_of\_threads** |                                                  Number of threads                                                 |               |

### Picard [AddOrReplaceReadGroups](https://github.com/msk-access/cwl-commandlinetools/tree/develop/picard_add_or_replace_read_groups_4.1.8.1)

|                     Argument Name                    |                   Summary                  | Default Value |
| :--------------------------------------------------: | :----------------------------------------: | :-----------: |
| **picard\_addRG\_read\_group\_sequencing\_platform** | Read-Group platform (e.g. ILLUMINA, SOLID) |               |
|  **picard\_addRG\_read\_group\_sequencing\_center**  |      Read-Group sequencing center name     |               |
|       **picard\_addRG\_read\_group\_run\_date**      |      Read-Group date in (Iso8601Date)      |               |
|    **picard\_addRG\_read\_group\_platform\_unit**    | Read-Group Platform Unit (eg. run barcode) |               |
|        **picard\_addRG\_read\_group\_library**       |             Read-Group library             |               |
|      **picard\_addRG\_read\_group\_identifier**      |                Read-Group ID               |               |
|      **picard\_addRG\_read\_group\_description**     |           Read-Group Description           |               |
|         **picard\_addRG\_output\_file\_name**        |            Output BAM file name            |               |
|            **picard\_addRG\_sort\_order**            |           Sort order for BAM file          |               |
|     **picard\_addRG\_read\_group\_sample\_name**     |           Read-Group sample name           |               |

### GATK [MergeBamAlignment](https://github.com/msk-access/cwl-commandlinetools/tree/develop/gatk_merge_bam_alignment_4.1.8.0)

|                    Argument Name                    |        Summary       | Default Value |
| :-------------------------------------------------: | :------------------: | :-----------: |
| **gatk\_merge\_bam\_alignment\_output\_file\_name** | Output BAM file name |               |

### bedtools [genomecov](https://github.com/msk-access/cwl-commandlinetools/tree/develop/bedtools_genomecov_v2.28.0_cv2)

|               Argument Name               |                                      Summary                                      | Default Value |
| :---------------------------------------: | :-------------------------------------------------------------------------------: | :-----------: |
| **bedtools\_genomecov\_option\_bedgraph** | option flag parameter to choose output file format. -bg refers to bedgraph format |               |

### bedtools [merge](https://github.com/msk-access/cwl-commandlinetools/tree/develop/bedtools_merge_v2.28.0_cv2)

|                   Argument Name                  |                                Summary                               | Default Value |
| :----------------------------------------------: | :------------------------------------------------------------------: | :-----------: |
| **bedtools\_merge\_distance\_between\_features** | Maximum distance between features allowed for features to be merged. |               |

### [ABRA2](https://github.com/msk-access/cwl-commandlinetools/tree/develop/abra2_2.22)

|            Argument Name            |                                                          Summary                                                         | Default Value |
| :---------------------------------: | :----------------------------------------------------------------------------------------------------------------------: | :-----------: |
|       **abra2\_window\_size**       |                           Processing window size and overlap (size,overlap) (default: 400,200)                           |               |
|    **abra2\_soft\_clip\_contig**    |  Soft clip contig args \[max*contigs,min\_base\_qual,frac* high\_qual\_bases,min\_soft\_clip\_len] (default:16,13,80,15) |               |
| **abra2\_scoring\_gap\_alignments** | Scoring used for contig alignments(match, mismatch\_penalty,gap\_open\_penalty,gap\_extend\_penalty) (default:8,32,48,1) |               |
|         **abra2\_no\_sort**         |                                            Do not attempt to sort final output                                           |               |
| **abra2\_no\_edge\_complex\_indel** |                                Prevent output of complex indels at read start or read end                                |               |
|  **abra2\_maximum\_mixmatch\_rate** |                       Max allowed mismatch rate when mapping reads back to contigs (default: 0.05)                       |               |
|  **abra2\_maximum\_average\_depth** |                    Regions with average depth exceeding this value will be downsampled (default: 1000)                   |               |
|      **abra2\_contig\_anchor**      |                  Contig anchor \[M\_bases\_at\_contig\_edge,max\_mismatches\_near\_edge] (default:10,2)                  |               |
|    **abra2\_consensus\_sequence**   |                        Use positional consensus sequence when aligning high quality soft clipping                        |               |

### Picard [FixMateInformation](https://github.com/msk-access/cwl-commandlinetools/tree/develop/picard_fix_mate_information_4.1.8.1)

|                     Argument Name                    |             Summary             | Default Value |
| :--------------------------------------------------: | :-----------------------------: | :-----------: |
| **picard\_fixmate\_information\_output\_file\_name** | The output BAM file to write to |               |

### Fgbio [FilterConsensusReads](https://github.com/msk-access/cwl-commandlinetools/tree/develop/fgbio_filter_consensus_reads_1.2.0)

| Argument Name                                                                           | Summary                                                                                                    | Default Value |
| --------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------- | ------------- |
| **fgbio\_filter\_consensus\_read\_reverse\_per\_base\_tags\_simplex\_duplex**           | Reverse \[complement] per base tags on reverse strand reads.- Simplex+Duplex                               |               |
| **fgbio\_filter\_consensus\_read\_reverse\_per\_base\_tags\_duplex**                    | Reverse \[complement] per base tags on reverse strand reads. - Duplex                                      |               |
| **fgbio\_filter\_consensus\_read\_require\_single\_strand\_agreement\_simplex\_duplex** | Mask (make N) consensus bases where the AB and BA consensus reads disagree (for duplex-sequencing only).   |               |
| f**gbio\_filter\_consensus\_read\_require\_single\_strand\_agreement\_duplex**          | Mask (make N) consensus bases where the AB and BA consensus reads disagree (for duplex-sequencing only).   |               |
| **fgbio\_filter\_consensus\_read\_max\_base\_error\_rate\_duplex**                      | The maximum error rate for a single consensus base. (Max 3 values) - Duplex                                |               |
| **fgbio\_filter\_consensus\_read\_max\_base\_error\_rate\_simplex\_duplex**             | The maximum error rate for a single consensus base. (Max 3 values) - Simplex + Duplex                      |               |
| **fgbio\_filter\_consensus\_read\_max\_no\_call\_fraction\_duplex**                     | Maximum fraction of no- calls in the read after filtering - Duplex                                         |               |
| **fgbio\_filter\_consensus\_read\_max\_read\_error\_rate\_duplex**                      | The maximum raw-read error rate across the entire consensus read. (Max 3 values) - Duplex                  |               |
| **fgbio\_filter\_consensus\_read\_max\_no\_call\_fraction\_simplex\_duplex**            | Maximum fraction of no- calls in the read after filtering - Simplex + Duplex                               |               |
| **fgbio\_filter\_consensus\_read\_max\_read\_error\_rate\_simplex\_duplex**             | The maximum raw-read error rate across the entire consensus read. (Max 3 values) - Simplex + Duplex        |               |
| **fgbio\_filter\_consensus\_read\_min\_base\_quality\_duplex**                          | Mask (make N) consensus bases with quality less than this threshold. - Dupelx                              |               |
| **fgbio\_filter\_consensus\_read\_min\_base\_quality\_simplex\_duplex**                 | Mask (make N) consensus bases with quality less than this threshold. - Simplex+Dupelx                      |               |
| **fgbio\_filter\_consensus\_read\_min\_mean\_base\_quality\_duplex**                    | The minimum mean base quality across the consensus read - Duplex                                           |               |
| **fgbio\_filter\_consensus\_read\_min\_mean\_base\_quality\_simplex\_duplex**           | The minimum mean base quality across the consensus read - Simplex + Duplex                                 |               |
| **fgbio\_filter\_consensus\_read\_min\_reads\_duplex**                                  | The minimum number of reads supporting a consensus base/read. (Max 3 values) - Duplex                      |               |
| **fgbio\_filter\_consensus\_read\_min\_reads\_simplex\_duplex**                         | <p>The minimum number of reads supporting a consensus base/read. (Max 3 values)</p><p>-Simplex+Duplex</p>  |               |
| **fgbio\_filter\_consensus\_read\_output\_file\_name\_simplex\_duplex**                 | Output BAM file name Simplex + Duplex                                                                      |               |
| **fgbio\_filter\_consensus\_read\_output\_file\_name\_duplex\_aln\_metrics**            | Output file name Duplex alignment metrics                                                                  |               |
| **fgbio\_filter\_consensus\_read\_output\_file\_name\_simplex\_aln\_metrics**           | Output file name Simplex alignment metrics                                                                 |               |
| **fgbio\_filter\_consensus\_read\_output\_file\_name\_duplex**                          | Output BAM file name - Duplex                                                                              |               |
| **fgbio\_filter\_consensus\_read\_min\_simplex\_reads**                                 | <p>The minimum number of reads supporting a consensus base/read. (Max 3 values) -</p><p>Simplex+Duplex</p> |               |

### Fgbio [Postprocessing](https://github.com/msk-access/cwl-commandlinetools/tree/develop/fgbio_postprocessing_simplex_filter_0.1.8)

|                      Argument Name                     |            Summary           | Default Value |
| :----------------------------------------------------: | :--------------------------: | :-----------: |
| **fgbio\_postprocessing\_output\_file\_name\_simplex** | Output BAM file name Simplex |               |

### Picard [CollectAlignmentSummaryMetrics](https://github.com/mskcc/cwl-commandlinetools/tree/develop/picard_collect_alignment_summary_metrics_2.8.1)

|                            Argument Name                           |                                  Summary                                  | Default Value |
| :----------------------------------------------------------------: | :-----------------------------------------------------------------------: | :-----------: |
| **gatk\_collect\_alignment\_summary\_metrics\_output\_file\_name** | Output file name for metrics on collapsed BAM (Duplex+Simplex+Singletons) |               |

## Template inputs file

{% code title="inputs.json" %}

```bash
{
    "abra2_consensus_sequence": null,
    "abra2_contig_anchor": null,
    "abra2_maximum_average_depth": null,
    "abra2_maximum_mixmatch_rate": null,
    "abra2_no_edge_complex_indel": true,
    "abra2_no_sort": null,
    "abra2_output_bams": "collapsed_abra.bam",
    "abra2_scoring_gap_alignments": null,
    "abra2_soft_clip_contig": null,
    "abra2_window_size": null,
    "bedtools_genomecov_option_bedgraph": true,
    "bedtools_merge_distance_between_features": null,
    "bwa_mem_K": 1000000,
    "bwa_mem_M": null,
    "bwa_mem_P": null,
    "bwa_mem_T": 30,
    "bwa_mem_Y": true,
    "bwa_mem_output": "test_collapsed_alignment.sam",
    "bwa_number_of_threads": null,
    "create_bam_index": true,
    "fgbio_call_duplex_consensus_reads_error_rate_post_umi": null,
    "fgbio_call_duplex_consensus_reads_error_rate_pre_umi": null,
    "fgbio_call_duplex_consensus_reads_max_reads_per_strand": null,
    "fgbio_call_duplex_consensus_reads_min_input_base_quality": null,
    "fgbio_call_duplex_consensus_reads_min_reads": [
        1,
        1,
        0
    ],
    "fgbio_call_duplex_consensus_reads_output_file_name": null,
    "fgbio_call_duplex_consensus_reads_read_group_id": "test",
    "fgbio_call_duplex_consensus_reads_read_name_prefix": null,
    "fgbio_call_duplex_consensus_reads_sort_order": null,
    "fgbio_call_duplex_consensus_reads_trim": null,
    "fgbio_collect_duplex_seq_metrics_description": null,
    "fgbio_collect_duplex_seq_metrics_duplex_umi_counts": true,
    "fgbio_collect_duplex_seq_metrics_intervals": null,
    "fgbio_collect_duplex_seq_metrics_mi_tag": null,
    "fgbio_collect_duplex_seq_metrics_min_ab_reads": null,
    "fgbio_collect_duplex_seq_metrics_min_ba_reads": null,
    "fgbio_collect_duplex_seq_metrics_output_prefix": null,
    "fgbio_filter_consensus_read_max_base_error_rate_duplex": null,
    "fgbio_filter_consensus_read_max_base_error_rate_simplex_duplex": null,
    "fgbio_filter_consensus_read_max_no_call_fraction_duplex": null,
    "fgbio_filter_consensus_read_max_no_call_fraction_simplex_duplex": null,
    "fgbio_filter_consensus_read_max_read_error_rate_duplex": null,
    "fgbio_filter_consensus_read_max_read_error_rate_simplex_duplex": null,
    "fgbio_filter_consensus_read_min_base_quality_duplex": 30,
    "fgbio_filter_consensus_read_min_base_quality_simplex_duplex": 30,
    "fgbio_filter_consensus_read_min_mean_base_quality_duplex": null,
    "fgbio_filter_consensus_read_min_mean_base_quality_simplex_duplex": null,
    "fgbio_filter_consensus_read_min_reads_duplex": [
        2,
        1,
        1
    ],
    "fgbio_filter_consensus_read_min_reads_simplex_duplex": [
        3,
        3,
        0
    ],
    "fgbio_filter_consensus_read_min_simplex_reads": null,
    "fgbio_filter_consensus_read_output_file_name_duplex": "collapsed_duplex.bam",
    "fgbio_filter_consensus_read_output_file_name_duplex_aln_metrics": null,
    "fgbio_filter_consensus_read_output_file_name_simplex_aln_metrics": null,
    "fgbio_filter_consensus_read_output_file_name_simplex_duplex": "collapsed_simplex-duplex.bam",
    "fgbio_filter_consensus_read_require_single_strand_agreement_duplex": true,
    "fgbio_filter_consensus_read_require_single_strand_agreement_simplex_duplex": null,
    "fgbio_filter_consensus_read_reverse_per_base_tags_duplex": true,
    "fgbio_filter_consensus_read_reverse_per_base_tags_simplex_duplex": true,
    "fgbio_group_reads_by_umi_assign_tag": null,
    "fgbio_group_reads_by_umi_edits": null,
    "fgbio_group_reads_by_umi_family_size_histogram": "group_reads_umi.hist.txt",
    "fgbio_group_reads_by_umi_include_non_pf_reads": null,
    "fgbio_group_reads_by_umi_input": {
        "class": "File",
        "path": "/Users/shahr2/Documents/test_reference/Uncollapsed_BAM_Generation_Output/test_fx.bam"
    },
    "fgbio_group_reads_by_umi_min_umi_length": null,
    "fgbio_group_reads_by_umi_output_file_name": null,
    "fgbio_group_reads_by_umi_raw_tag": null,
    "fgbio_group_reads_by_umi_strategy": "paired",
    "fgbio_postprocessing_output_file_name_simplex": "collapsed_simplex.bam",
    "gatk_collect_alignment_summary_metrics_output_file_name": null,
    "gatk_merge_bam_alignment_output_file_name": null,
    "gatk_sam_to_fastq_include_non_pf_reads": null,
    "gatk_sam_to_fastq_include_non_primary_alignments": null,
    "gatk_sam_to_fastq_output_name_R1": "test_fx_group_cons_R1.fastq.gz",
    "gatk_sam_to_fastq_output_name_R2": "test_fx_group_cons_R2.fastq.gz",
    "gatk_sam_to_fastq_output_name_unpaired": null,
    "picard_addRG_sort_order": "queryname",
    "picard_addRG_output_file_name": null,
    "picard_addRG_read_group_description": null,
    "picard_addRG_read_group_identifier": "test",
    "picard_addRG_read_group_library": "test",
    "picard_addRG_read_group_platform_unit": "IDT11",
    "picard_addRG_read_group_run_date": null,
    "picard_addRG_read_group_sample_name": "MSKCC",
    "picard_addRG_read_group_sequencing_center": "ILLUMINA",
    "picard_addRG_read_group_sequencing_platform": "test",
    "picard_fixmate_information_output_file_name": "collapsed_fx.bam",
    "reference_sequence": {
        "class": "File",
        "path": "/Users/shahr2/Documents/test_reference/test_uncollapsed_bam_generation/reference/chr14_chr16.fasta"
    },
    "sort_order": "coordinate",
    "validation_stringency": "LENIENT"
}
```

{% endcode %}
