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File types

Learning outcomes

After having completed this chapter you will be able to:

  • Describe the fasta and fastq file format
  • Describe which information can be stored in a standard Illumina fastq title
  • Reproduce how and why base quality is stored in a fastq file as a single ASCII character
  • Lookup relevant information of an alignment in the header of a sam file
  • Describe what information is stored in each column of a sam file
  • Describe how information is stored in a sam flag
  • Describe the bed and gtf file format
  • Describe vcf file format


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