disambiguateFor mixed or explant samples, provide a list of
genome_buildidentifiers to check and remove from alignment. Currently supports cleaning a single organism. For example, with
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
staris chosen as the aligner. Aligner must be set to a non false value for this to run.
details: - 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 tools_on: - noalt_calling variantcaller: - vardict - mutect2 vcfanno: somatic analysis: variant2 description: SAMPLE files: - /path/to/project/input/sample_1.fq.gz - /path/to/project/input/sample_2.fq.gz genome_build: hg38 metadata: batch: bSAMPLE phenotype: tumor upload: dir: ../final
final/project/multiqc/multiqc_report.html will contain hg38 and mm10 columns with numbers of reads aligned to hg38 and mm10.
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.).