QC.md

Quality control (QC) steps

NAIC Accelerated Genomics implements QC steps on raw reads (FASTQ) used as input and alignment files generated in intermediate steps of the Germline pipeline. These QC processes are run on CPU platforms.

QC pipeline workflow

graph TD;
   i1(Raw data - FASTQ) --> 1
   1(FASTQC)
   i2(Alignment file used for variant calling - BAM) --> 2
   i2(Alignment file used for variant calling - BAM) --> 3
   i2(Alignment file used for variant calling - BAM) --> 4
   i2(Alignment file used for variant calling - BAM) --> 5
   i2(Alignment file used for variant calling - BAM) --> 6
   2(SAMTools FLAGSTAT)
   3(SAMTools STAT)
   4(Mosdepth)
   5(GATK CollectInsertSummaryMatrices)
   6(GATK CollectAlignmentSummaryMatrices)
   1 --> 7
   2 --> 7
   3 --> 7
   4 --> 7
   5 --> 7
   6 --> 7
   7(MultiQC report)

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   classDef white fill:#ffffff;
   class 1,2,3,4,5,6,7 highlight;

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Processes in QC pipeline

• FASTQC - https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
• SAMtools flagstat - https://www.htslib.org/doc/samtools-flagstat.html
• SAMtools stat - https://www.htslib.org/doc/samtools-stats.html
• Mosdepth - https://github.com/brentp/mosdepth
• GATK CollectInsertSizeMetrics - https://gatk.broadinstitute.org/hc/en-us
• GATK collectAlignmentSummaryMetrics - https://gatk.broadinstitute.org/hc/en-us
• MultiQC - https://multiqc.info/

Versions in QC pipeline

• Mosdepth: 0.3.3--h37c5b7d_2
• FASTQC: 0.12.1
• SAMTools: 1.18
• GATK: 4.3.0.0
• MultiQC: 1.19