4.29. detect_cross_contamination¶
Detect cross-contamination between samples using consensus-level and sub-consensus variation.
4.29.1. Inputs¶
4.29.1.1. Required inputs¶
detect_cross_contamination.aligned_bams
Array[File]+ — Default: None
reads aligned to the sequence within reference_fasta.
detect_cross_contamination.genome_fastas
Array[File]+ — Default: None
consensus sequences, one per file in aligned_bams, in corresponding order
detect_cross_contamination.reference_fasta
File — Default: None
Reference genome to which reads have be aligned, needed here for variant calling
4.29.1.2. Other inputs¶
Show/Hide
detect_cross_contamination.depth.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
detect_cross_contamination.depth.out_basename
String — Default: basename(aligned_bam,'.bam')
???
detect_cross_contamination.detect_cross_contam.compare_diagonal_neighbors
Boolean? — Default: false
Compare diagonal plate neighbors (top-right, bottom-right, top-left, bottom-left)
detect_cross_contamination.detect_cross_contam.compare_direct_neighbors
Boolean? — Default: true
Compare direct plate neighbors (left, right, top, bottom)
detect_cross_contamination.detect_cross_contam.compare_full_column
Boolean? — Default: false
Compare samples in the same column (e.g., column 8)
detect_cross_contamination.detect_cross_contam.compare_full_plate
Boolean? — Default: false
Compare all samples in the same plate map
detect_cross_contamination.detect_cross_contam.compare_full_row
Boolean? — Default: false
Compare samples in the same row (e.g., row A)
detect_cross_contamination.detect_cross_contam.docker
String — Default: "quay.io/broadinstitute/polyphonia:latest"
???
detect_cross_contamination.detect_cross_contam.max_mismatches
Int — Default: 1
Maximum allowed bases in contaminating sample consensus not matching contaminated sample alleles
detect_cross_contamination.detect_cross_contam.min_genome_coverage
Float — Default: 0.95
Minimum proportion genome covered for a sample to be included
detect_cross_contamination.detect_cross_contam.min_maf
Float — Default: 0.03
Minimum minor allele frequency for position to be considered heterozygous
detect_cross_contamination.detect_cross_contam.min_read_depth
Int — Default: 100
Minimum read depth for a position to be used for comparison
detect_cross_contamination.detect_cross_contam.min_readcount
Int — Default: 10
Minimum minor allele readcount for position to be considered heterozygous
detect_cross_contamination.detect_cross_contam.out_basename
String — Default: "potential_cross_contamination"
???
detect_cross_contamination.detect_cross_contam.plate_columns
Int? — Default: None
Number columns in plate (e.g., 1, 2, 3, 4)
detect_cross_contamination.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.detect_cross_contam.plate_rows
Int? — Default: None
Number rows in plate (e.g., A, B, C, D)
detect_cross_contamination.detect_cross_contam.plate_size
Int? — Default: 96
Standard plate size (6-well, 12-well, 24, 48, 96, 384, 1536, 3456)
detect_cross_contamination.detect_cross_contam.print_all
Boolean? — Default: false
Output outcomes of all comparisons (all comparisons are marked as potential cross-contamination)
detect_cross_contamination.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.lofreq.docker
String — Default: "quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4"
???
detect_cross_contamination.lofreq.out_basename
String — Default: basename(aligned_bam,'.bam')
???
4.29.2. Outputs¶
detect_cross_contamination.contamination_figures
Array[File]
???
detect_cross_contamination.contamination_report
File
???
detect_cross_contamination.lofreq_vcfs
Array[File]
???
detect_cross_contamination.lofreq_version
String
???
detect_cross_contamination.read_depths
Array[File]
???
Generated using WDL AID (1.0.0)