4.30. detect_cross_contamination_precalled_vcfs

Detect cross-contamination between samples using consensus-level and sub-consensus variation, from consensus genomes and pre-called LoFreq vcf files.

4.30.1. Inputs

4.30.1.1. Required inputs

detect_cross_contamination_precalled_vcfs.genome_fastas
Array[File]+ — Default: None
consensus sequences, one per file in aligned_bams, in corresponding order

detect_cross_contamination_precalled_vcfs.lofreq_vcfs
Array[File]+ — Default: None
per-sample variant call files (VCF) called by LoFreq against reference_fasta

detect_cross_contamination_precalled_vcfs.reference_fasta
File — Default: None
Reference genome to which reads have been aligned, needed here for variant calling

4.30.1.2. Other inputs

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detect_cross_contamination_precalled_vcfs.detect_cross_contam.compare_diagonal_neighbors
Boolean? — Default: false
Compare diagonal plate neighbors (top-right, bottom-right, top-left, bottom-left)

detect_cross_contamination_precalled_vcfs.detect_cross_contam.compare_direct_neighbors
Boolean? — Default: true
Compare direct plate neighbors (left, right, top, bottom)

detect_cross_contamination_precalled_vcfs.detect_cross_contam.compare_full_column
Boolean? — Default: false
Compare samples in the same column (e.g., column 8)

detect_cross_contamination_precalled_vcfs.detect_cross_contam.compare_full_plate
Boolean? — Default: false
Compare all samples in the same plate map

detect_cross_contamination_precalled_vcfs.detect_cross_contam.compare_full_row
Boolean? — Default: false
Compare samples in the same row (e.g., row A)

detect_cross_contamination_precalled_vcfs.detect_cross_contam.docker
String — Default: "quay.io/broadinstitute/polyphonia:latest"
???

detect_cross_contamination_precalled_vcfs.detect_cross_contam.max_mismatches
Int — Default: 1
Maximum allowed bases in contaminating sample consensus not matching contaminated sample alleles

detect_cross_contamination_precalled_vcfs.detect_cross_contam.min_genome_coverage
Float — Default: 0.95
Minimum proportion genome covered for a sample to be included

detect_cross_contamination_precalled_vcfs.detect_cross_contam.min_maf
Float — Default: 0.03
Minimum minor allele frequency for position to be considered heterozygous

detect_cross_contamination_precalled_vcfs.detect_cross_contam.min_read_depth
Int — Default: 100
Minimum read depth for a position to be used for comparison

detect_cross_contamination_precalled_vcfs.detect_cross_contam.min_readcount
Int — Default: 10
Minimum minor allele readcount for position to be considered heterozygous

detect_cross_contamination_precalled_vcfs.detect_cross_contam.out_basename
String — Default: "potential_cross_contamination"
???

detect_cross_contamination_precalled_vcfs.detect_cross_contam.plate_columns
Int? — Default: None
Number columns in plate (e.g., 1, 2, 3, 4)

detect_cross_contamination_precalled_vcfs.detect_cross_contam.plate_maps
Array[File]? — Default: None
Optional plate map(s) (tab-separated, no header: sample name, plate position (e.g., A8))

detect_cross_contamination_precalled_vcfs.detect_cross_contam.plate_rows
Int? — Default: None
Number rows in plate (e.g., A, B, C, D)

detect_cross_contamination_precalled_vcfs.detect_cross_contam.plate_size
Int? — Default: 96
Standard plate size (6-well, 12-well, 24, 48, 96, 384, 1536, 3456)

detect_cross_contamination_precalled_vcfs.detect_cross_contam.print_all
Boolean? — Default: false
Output outcomes of all comparisons (all comparisons are marked as potential cross-contamination)

detect_cross_contamination_precalled_vcfs.detect_cross_contam.print_all_isnvs
Boolean? — Default: true
Include all threshold-passing samples in iSNVs visualizations, including samples without plate neighbors

detect_cross_contamination_precalled_vcfs.detect_cross_contam.read_depths
Array[File]? — Default: None
Read depth tables (tab-separated, no header: reference name, position, read depth); provide alongside vcf files or heterozygosity tables if min-depth>0

4.30.2. Outputs

detect_cross_contamination_precalled_vcfs.contamination_figures
Array[File]
???

detect_cross_contamination_precalled_vcfs.contamination_report
File
???

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