# Phase 2 Whole Exome Sequencing +++ Overview # Overview Phase 2 HTAN data standards for Whole Exome Sequencing (WES) are similar to those implemented in Phase 1 under the assay type "Bulk DNA-seq". Metadata requirements are documented in the HTAN Data Model readthedocs pages. This part of the manual describes **file requirements** for Whole Exome Sequencing data. +++ Data Levels ## Data Levels WES data has 3 levels. Table 1 HTAN Data Levels for WES Data | Level | Definition | Example Data | |-------|------------|--------------| | 1 | Raw data | FASTQs, Unaligned BAMs | | 2 | Aligned primary data | Aligned BAMs | | 3 | Derived biomolecular data | VCFs (mafs optional) | +++ Reference and Annotation Versions ## Genomic Reference and Annotation Version HTAN data contributors must provide the genomics reference and annotation version used for any aligned sequencing files. This information can be found in the level 2 metadata. HTAN strongly recommends using GENCODE/Ensembl genome annotations for level 2 sequencing data. +++ File Requirements ## File Requirements !!! Terminology: This document uses the following terms from IEFT RFC 2119 MUST / REQUIRED / SHALL: ✅ (denotes absolute requirement) MUST NOT / SHALL NOT: ❌ (denotes absolute prohibition) SHOULD / RECOMMENDED: 🌟 (denotes recommendation) SHOULD NOT / NOT RECOMMENDED: :no_good: (denotes not recommended) MAY / OPTIONAL: :woman-shrugging: (denotes optional) !!! **Level 1** \ ✅ FASTQ files or Unaligned BAM files MUST be submitted for all sequencing data.\ ✅ Each FASTQ or Unaligned BAM file MUST have a single record (row) in the manifest. **Level 2** \ ✅ Level 2 data MUST be submitted if alignment was performed. **Level 3** \ ✅ Level 3 DNA-seq files MUST include a vcf file containing called variants.\ 🌟 Level 3 DNA-seq files SHOULD include a seg file if copy number variation was assessed.\ :woman-shrugging: Submission of maf files is OPTIONAL.