Section 3 Validate NGS data

3.1 Step 1

• Use woofr::validation_outputs to generate a TSV file with the following columns:
  • col1 - type of file
    1. VCF
    2. BAM
    3. FASTQ
    4. Other
  • col2 - path to file

3.2 Step 2

• Now we can iterate through each row of the TSV according to its type:
  • VCF:
    • head
    • vcf-validator
  • BAM:
    • samtools quickcheck
    • GATK ValidateSamFile link1, link2
    • UMich BamUtil validate
  • FASTQ:
    • fqtools validate

3.3 Output

woof-validation1/final
    |--- vcf/
         |--- tool_1/
              |--- results_fileA.txt
              |--- results_fileB.txt
         |--- tool_2/
              |--- results_fileA.txt
              |--- results_fileB.txt
    |--- bam/
         |--- tool_1/
              |--- results_fileC.txt
              |--- results_fileD.txt
         |--- tool_2/
              |--- results_fileC.txt
              |--- results_fileD.txt
    |--- fastq/
         |--- tool_1/
              |--- results_fileE.txt
              |--- results_fileF.txt
         |--- tool_2/
              |--- results_fileE.txt
              |--- results_fileF.txt
    |--- md5/
         |--- vcf/
              |--- md5_fileA.txt
              |--- md5_fileB.txt
         |--- bam/
              |--- md5_fileC.txt
              |--- md5_fileD.txt
         |--- fastq/
              |--- md5_fileE.txt
              |--- md5_fileF.txt
         |--- other/
              |--- md5_fileG.txt
              |--- md5_fileH.txt