Description

generate VCF file from a BAM file using various calling methods

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

3 ()

4 ()

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

Output

Name
Description
Pattern

0 ()

0 ()

Tools

atlas Documentation

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

https://bitbucket.org/wegmannlab/atlasdoi: 10.1101/105346License: GPL v3
Authors