# Optional: Change software versions and dependencies of the VCPA workflow

**VCPA is functional equivalent to the CCDG/TOPMed protocol. VCPA is built upon the following default software versions and dependency files for variant call. We strongly recommend users to use these default versions.**

Users can still change the default software versions using the JSON file if needed - see example shown at the bottom of the page.

### **Software**

[BWA](https://github.com/lh3/bwa/releases/tag/v0.7.15) (version 0.7.15)

[SAMTOOLS](https://github.com/samtools/samtools/releases/tag/1.3.1) (version: 1.3.1-42-g0a15035(using htslib 1.3.2-135-g50db54b))

[GATK](https://software.broadinstitute.org/gatk/download/) (version 3.7)

[PICARD](https://github.com/broadinstitute/picard/releases/tag/2.8.1) (version 2.8.1)

[SAMBABA](https://github.com/broadinstitute/picard/releases/tag/2.8.1) (version v0.6.5)

[SAMBLASTER](https://github.com/GregoryFaust/samblaster/releases/tag/v.0.1.24) (version 0.1.12b)

[VCFTOOLS](https://sourceforge.net/projects/vcftools/files/) (version 0.1.12b)

[BAMUTIL](https://github.com/statgen/bamUtil/tree/NonPrimaryDedup) (version v1.0.13)

[BCFTOOLS](https://github.com/samtools/bcftools/releases/tag/1.3.1) (version: 1.3.1-1)

### Dependency files

> **Hg38 Reference genome version GRCh38DH**

* 1000 Genomes Project [version](ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa) (3366 contigs)
* md5sum: *64b32de2fc934679c16e83a2bc072064*

> **GATK variant call hg38 dependency files**

* **dbSNP annotation**

  [dbSNP 138 lifted SNV file](https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf) \[ [Corresponding index file](https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx) ]
* **Indels annotation**

  [dbSNP 138 lifted Indel file](https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz) \[ [Corresponding index file](https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi) ]

  [Mills and 1000G gold standard indels file](https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz) \[ [Corresponding index file](https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi) ]

The example of JSON file: 

```
Tutorial_vcpa_steps.ref_alt : ## Path of the FASTA.alt alignment file
Tutorial_vcpa_steps.ref_amb : ## Path of the FASTA.amb alignment file
Tutorial_vcpa_steps.ref_ann : ## Path of the FASTA.ann alignment file
Tutorial_vcpa_steps.ref_bwt : ## Path of the FASTA.bwt alignment file
Tutorial_vcpa_steps.ref_pac : ## Path of the FASTA.pac alignment file
Tutorial_vcpa_steps.ref_sa :  ## Path of the FASTA.sa alignment file
Tutorial_vcpa_steps.ref_fai : ## Path of the FASTA.fai alignment file
Tutorial_vcpa_steps.ref_dict :  ## Path of the FASTA.dict alignment file
Tutorial_vcpa_steps.input_bam :  ## Path of the BAM/CRAM file 
Tutorial_vcpa_steps_steps.fastq_directory_path :  ## Path for the FASTQ file 
Tutorial_vcpa_steps.ref_fasta :  ## Path of the reference genome FASTA file 
Tutorial_vcpa_steps.TARGET : ## Path of the WES capture kit / target region file 
Tutorial_vcpa_steps.KNOWN : ## Path of the dbSNP 138 lifted Indel file 
Tutorial_vcpa_steps.KNOWN_index : ## Path of the dbSNP 138 lifted Indel index file
Tutorial_vcpa_steps.DBSNP : ## Path of the dbSNP 138 lifted SNV file
Tutorial_vcpa_steps.DBSNP_index :  ## Path of the dbSNP 138 lifted SNV index file
Tutorial_vcpa_steps.GOLD : ## Path of the Mills and 1000G gold standard indels file
Tutorial_vcpa_steps.GOLD_index : ## Path of the Mills and 1000G gold standard indels index file
Tutorial_vcpa_steps.BWA : ## Location of the BWA software
Tutorial_vcpa_steps.SAMBAMBA : ## Location of the SAMBAMBA software
Tutorial_vcpa_steps.SAMBLASTER : ## Location of the SAMBLASTER software
Tutorial_vcpa_steps.SAMTOOLS : ## Location of the SAMTOOLS software
Tutorial_vcpa_steps.PICARD : ## Location of the PICARD software
Tutorial_vcpa_steps.bamUtil : ## Location of the bamUtil software
Tutorial_vcpa_steps.GATK : ## Location of the GATK software
Tutorial_vcpa_steps.tmp : ## Location of the template
Tutorial_vcpa_steps.log : ## Location of the logs
```


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://niagads.gitbook.io/vcpa/optional-change-software-versions-and-dependencies-of-the-vcpa-workflow.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.