Understanding the implications of initiating analyses from FASTQ versus VCF files in VarSome Clinical.
In VarSome Clinical, users have the flexibility to initiate analyses using either FASTQ or VCF files, each offering distinct workflows and outcomes.
Starting from FASTQ Files:
FASTQ files contain raw sequencing data, including both nucleotide sequences and their corresponding quality scores. Initiating an analysis from FASTQ files allows VarSome Clinical to perform comprehensive end-to-end processing, which includes:
- Alignment: Mapping sequencing reads to a reference genome.
- Variant Calling: Identifying single nucleotide variants (SNVs), insertions, deletions, and copy number variations (CNVs).
- Annotation and Classification: Providing detailed information and pathogenicity assessments for identified variants.
This approach ensures that all analytical steps adhere to VarSome Clinical's standardized pipelines, potentially leading to more consistent and reliable results. Additionally, starting from FASTQ files enables the detection of a broader range of variants, including structural variants, which might be missed when starting from VCF files.
Starting from VCF Files:
VCF (Variant Call Format) files contain pre-identified variants without the accompanying raw sequencing data. When initiating an analysis from VCF files, VarSome Clinical focuses on:
- Annotation and Classification: Providing detailed information and pathogenicity assessments for the variants listed in the VCF.
This method is suitable when variant calling has already been performed, and the primary goal is to annotate and classify known variants. However, it's important to note that the quality and comprehensiveness of the analysis are contingent upon the accuracy and completeness of the provided VCF file. Potential limitations include:
- Variant Detection: The platform cannot identify variants that may have been missed during the external variant calling process.
- Filtering Parameters: It lacks insight into the specific parameters or filters applied during the creation of the VCF, which may affect the comprehensiveness and accuracy of the variant data.
When starting analyses from VCF, VarSome Clinical is not responsible for any missed variants or the specific filtering criteria applied during the initial variant calling.
In summary, choosing between FASTQ and VCF files as starting points in VarSome Clinical depends on the specific needs of your analysis. For comprehensive analysis with full control over variant detection and quality assessment, starting from FASTQ files is recommended. If variant calling has already been performed and the focus is on annotating known variants, starting from VCF files may be appropriate.