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:file
The BAI file for the input BAM file
*.bai
pmd:file
Optional PMD file from atlas pmd function in text format
*.txt
recal:file
Optional recalibration file from atlas recal function in text format
fasta:file
The reference FASTA file used to generate the BAM file
*.{fasta,fna,fa}
fai:file
The index of the FASTA file used for to generate the BAM file
*.fai
known_alleles:file
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:file
VCF file with variant calls
*.vcf.gz
versions
versions.yml:file
File containing software versions
versions.yml
ATLAS, a suite of methods to accurately genotype and estimate genetic diversity
