generate VCF file from a BAM file using various calling methods
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam
:file
A BAM/ file
*.bam
bai
The BAI file for the input BAM file
*.bai
pmd
Optional PMD file from atlas pmd function in text format
*.txt
recal
Optional recalibration file from atlas recal function in text format
fasta
The reference FASTA file used to generate the BAM file
*.{fasta,fna,fa}
fai
The index of the FASTA file used for to generate the BAM file
*.fai
known_alleles
Optional tab separated text file containing 1-based list of known alleles. See atlas call documentation.
*.{txt.tsv}
method
:string
Which variant calling algorithm to use. Some may require additional parameters supplied via ext.args. Check atlas documentation.
MLE|Bayesian|allelePresence|randomBase|majorityBase
vcf
*.vcf.gz
VCF file with variant calls
versions_atlas
${task.process}
The name of the process
atlas
The name of the tool
(atlas 2>&1) | grep Atlas | head -n 1 | sed -e 's/^[[:space:]]*Atlas //'
:eval
The expression to obtain the version of the tool
versions
ATLAS, a suite of methods to accurately genotype and estimate genetic diversity
