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ngs-bits

note

Calculating statistics from FASTQ, BAM, and VCF.

https://github.com/imgag/ngs-bits

The ngs-bits module parses XML output generated for several tools in the ngs-bits collection:

  • ReadQC for statistics on FASTQ files,
  • MappingQC for statistics on BAM files,
  • SampleGender for gender prediction based on sequencing data.

File search patterns​

ngsbits/mappingqc:
  - contents: MappingQC
    fn: "*.qcML"
    num_lines: 20
ngsbits/readqc:
  - contents: ReadQC
    fn: "*.qcML"
    num_lines: 20
  - contents: SeqPurge
    fn: "*.qcML"
    num_lines: 20
ngsbits/samplegender:
  - fn: "*_ngsbits_sex.tsv"