generate VCF file from a BAM file using various calling methods
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
A BAM/ file
*.bam
bai{:bash}
The BAI file for the input BAM file
*.bai
pmd{:bash}
Optional PMD file from atlas pmd function in text format
*.txt
recal{:bash}
Optional recalibration file from atlas recal function in text format
fasta{:bash}
The reference FASTA file used to generate the BAM file
*.{fasta,fna,fa}
fai{:bash}
The index of the FASTA file used for to generate the BAM file
*.fai
known_alleles{:bash}
Optional tab separated text file containing 1-based list of known alleles. See atlas call documentation.
*.{txt.tsv}
method{:bash}
: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{:bash}
*.vcf.gz{:bash}
VCF file with variant calls
*.vcf.gz
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
ATLAS, a suite of methods to accurately genotype and estimate genetic diversity
