# Input Checks

## Input Validation Steps

In addition to sample sheet validation, before starting an analysis, the software performs the following checks:

* Resource bundle integrity
* DRAGEN license validity
* NEW in v2.6.3! Instrument Type determination

Instrument type is required by the software because different instrument platforms produce output with distinct systematic noise profiles. DRAGEN TSO 500 ctDNA analysis software requires instrument-specific baseline noise files. Before kicking off analysis, the software determines the instrument type in order to select which baseline files to use. This means that even when starting from FASTQ, all samples in the run must be sequenced on the same type of instrument.

## Instrument Type Determination for Baselines

When starting analysis from BCL files, the software references the `RunInfo.xml` file in the Run folder to identify the sequencing instrument type. For analyses beginning with FASTQ files, the software reads the FASTQ file headers for this information.

<table><thead><tr><th width="539.0443725585938">Instrument Serial Number Prefix</th><th>Instrument Type</th></tr></thead><tbody><tr><td>A</td><td>NovaSeq6000</td></tr><tr><td>ADX</td><td>NovaSeq6000Dx</td></tr><tr><td>VH</td><td>NextSeq1k2k</td></tr><tr><td>LH</td><td>NovaSeqXPlus</td></tr><tr><td>LL</td><td>NovaSeqX</td></tr></tbody></table>

{% hint style="danger" %}
For analysis starting from FASTQ files, if a mixed instrument type is detected, the software will exit with an error.
{% endhint %}

**The Combined Variant Output File will include the instrument type** [combined-variant-output](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-output/combined-variant-output "mention")

Systematic Noise files for certain variant types depend on library prep kit, instrument type, or both. The software will select the correct set of resource files (systematic noise, panel of normals) according to its determination of instrument type and library prep kit. VCF headers contain details on which resource files were used in the analysis.

* Library Preparation Kit: TSO500 ctDNA v2 (index length: 10)
  * Instrument Type&#x73;**:**
    * NovaSeq 6000, NovaSeq 6000Dx: Use one set of baselines.
    * NextSeq 1000/ 2000: Use a different set of baselines.
    * NovaSeqX, NovaSeqXPlus: Use another set of baselines.
* Library Preparation Kit: TSO500 ctDNA (index length: 8)
  * A single set of baselines applies to all instrument types.

{% hint style="warning" %}
If instrument type is undetermined (ie not matching any of the below), the software will set instrument type to NA, and the baselines for NovaSeq 6000 and NovaSeq 6000Dx will be applied.
{% endhint %}

{% hint style="warning" %}
If the software cannot detect the Library Prep Kit due to a missing index in the sample sheet, it will default to TSO500 ctDNA v2.
{% endhint %}