ngs-bits

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"