Solid¶

Description¶

The input data for the pipeline consists of fastq files. However, for the pipeline to consume the data, it needs to be provided in the form of a CSV file that includes metadata...

Input CSV¶

Column Descriptions¶

• sample_id: Text representing the name or id of the sample being analyzed
• type: Type of the sample, e.g., tumor or normal
• assay: Assay of the sample, e.g., tumorWGS, myeloid, solidtumor, etc.
• platform: Name of the platform used for sequencing, e.g., illumina
• read1: Full path to the read 1 fastq file
• read2: Full path to the read 2 fastq file

Output Files¶

• BAM: A BAM file is a compressed binary file format used to store and index high-throughput sequencing data, such as DNA sequence reads aligned to a reference genome
• VCF: A VCF file is a text file format used to store and annotate genetic variation data, such as single nucleotide polymorphisms (SNPs) and small insertions/deletions (indels), identified from sequencing data.
• HTML_Report: An HTML documentation report is a text-based file format used to present information in a web browser, including text, images, and hyperlinks, typically used for displaying project documentation and results
• Markdown_Files: A Markdown file is a lightweight markup language used to format and structure plain text documents, often used for creating documentation, README files, and notes

Software Versions¶