NGS Data Analysis: Is there any method to detect all non-callable variants from the data file?

01 January 2015 1 497 Report

Non-callable variants cause a problem during the processing of the NGS data. Is there any method to detect all non-callable variants from the data file?

Michael B Black

There are two pipelines I know of that evaluate non-callable regions in a genome after read-mapping:

GATK from the broad: https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_coverage_CallableLoci.php

and the BCBio-NextGen pipeline: http://bcb.io/page/2/?app-download=ios (and source is at https://github.com/chapmanb/bcbio-nextgen).

BCBio is a python toolkit, while GATK is built on Java (and it sometimes uses R tools for generating graphics).

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