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
BAI file
*.bai
empiric
Optional txt file from PMD estimations (atlas/pmd)
*.txt
readgroups
read groups
alleles
Optional bed file with known alleles
*.bed
invariant_sites
Optional bed file with invariant site coordinates
recal_patterns
file containing the sequencing bias for each of the Read Group pools
versions_atlas
${task.process}
:string
The name of the process
atlas
The name of the tool
((atlas 2>&1) | grep Atlas | head -n 1 | sed -e 's/^[ ]*Atlas //')
:eval
The expression to obtain the version of the tool
versions
ATLAS, a suite of methods to accurately genotype and estimate genetic diversity
