Gives an estimation of the sequencing bias based on known invariant sites
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
BAM file
*.bam
bai{:bash}
BAI file
*.bai
empiric{:bash}
Optional txt file from PMD estimations (atlas/pmd)
*.txt
readgroups{:bash}
read groups
alleles{:bash}
Optional bed file with known alleles
*.bed
invariant_sites{:bash}
Optional bed file with invariant site coordinates
recal_patterns{:bash}
*.txt{:bash}
file containing the sequencing bias for each of the Read Group pools
versions_atlas{:bash}
${task.process}{:bash}
:string
The name of the process
atlas{:bash}
The name of the tool
((atlas 2>&1) | grep Atlas | head -n 1 | sed -e 's/^[ ]*Atlas //'){:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
ATLAS, a suite of methods to accurately genotype and estimate genetic diversity
