Overview

majorityBaseCaller chooses the base with the most occurences out of all sequenced bases covering given site of the genome. If two bases are equally current, one of them is chosen at random. This caller produces haploid calls, which can subsequently be turned into "pseudo-diploid" calls by duplicating the random base. This type of calls is usually used to reduce reference bias. ATLAS is not affected by reference bias and we suggest to use our more sophisticated allelePresence caller if the sequencing data is too scarce for diploid calls.

Input

• BAM file
• FASTA file

Output

The output is a gzipped .txt format.

Each line represents a position in the genome and the columns provide the following information:

• Chromosome
• Position on chromosome
• Reference base (if no reference file was passed the reference base will always be 'N')
• Pileup of all bases
• The random base chosen

Usage Example

The required syntax to launch ATLAS as the majorityBaseCaller is:

.. sourcecode:: bash

./atlas task=majorityBaseCaller bam=example.bam

Specific Arguments

• fasta : The reference file is optional but without it the reference bases will not be printed.
• printAll : Print all sites, also the ones with sequencing depth=0.

Engine Parameters

Engine parameters that are common to all tasks can be found here.