Description

generate VCF file from a BAM file using various calling methods

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

bam (file)

A BAM/ file

*.bam

bai (file)

The BAI file for the input BAM file

*.bai

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

recal (file)

Optional recalibration file from atlas recal function in text format

*.txt

pmd (file)

Optional PMD file from atlas pmd function in text format

*.txt

known_alleles (file)

Optional tab separated text file containing 1-based list of known alleles. See atlas call documentation.

*.{txt.tsv}

method (character)

Which variant calling algorithm to use. Some may require additional parameters supplied via ext.args. Check atlas documentation.

MLE|Bayesian|allelePresence|randomBase|majorityBase

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

bam (file)

VCF file with variant calls

*.vcf.gz
author
Github user jfy133
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Tools

atlas
GPL v3

ATLAS, a suite of methods to accurately genotype and estimate genetic diversity

bitbucket.org/wegmannlab/atlas/wiki https://bitbucket.org/wegmannlab/atlas 10.1101/105346