• disambiguate For mixed or explant samples, provide a list of genome_build identifiers to check and remove from alignment. Currently supports cleaning a single organism. For example, with genome_build: hg19 and disambiguate: [mm10], it will align to hg19 and mm10, run disambiguation and discard reads confidently aligned to mm10 and not hg19. Affects fusion detection when star is chosen as the aligner. Aligner must be set to a non false value for this to run.

Example config:

- algorithm:
    aligner: bwa
    background: /path/to/project/config/1000g_pon.hg38.vcf.gz
    disambiguate: mm10
    mark_duplicates: true
    platform: illumina
    quality_format: standard
    realign: false
    recalibrate: false
    remove_lcr: true
    - noalt_calling
    - vardict
    - mutect2
    vcfanno: somatic
  analysis: variant2
  description: SAMPLE
  - /path/to/project/input/sample_1.fq.gz
  - /path/to/project/input/sample_2.fq.gz
  genome_build: hg38
    batch: bSAMPLE
    phenotype: tumor
  dir: ../final

The resulting final/project/multiqc/multiqc_report.html will contain hg38 and mm10 columns with numbers of reads aligned to hg38 and mm10. Also final/sample contains sample-ready.bam - reads aligned to hg38 and sample-disambiguate-mm10.bam - reads aligned to mm10.


  • final/project/multiqc: Reads = single reads in the final bam (mapped to human genome), hg38 = single reads mapped to human genome (same as Reads), mm10 = single reads mapped to mouse genome; Ambig. = single reads ambiguously mapped; Total reads = sum (hg38 + mm10 + Ambig.).