Gives an estimation of the sequencing bias based on known invariant sites
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam:file
BAM file
*.bam
bai:file
BAI file
*.bai
empiric:file
Optional txt file from PMD estimations (atlas/pmd)
*.txt
readgroups:file
read groups
alleles:file
Optional bed file with known alleles
*.bed
invariant_sites:file
Optional bed file with invariant site coordinates
recal_patterns
*.txt:file
file containing the sequencing bias for each of the Read Group pools
versions
versions.yml:file
File containing software versions
versions.yml
ATLAS, a suite of methods to accurately genotype and estimate genetic diversity
