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Add option to set VCF ID field value, this can be used to ID germline variants for SnpSift
author Jim Johnson <jj@umn.edu>
date Thu, 11 Apr 2013 10:28:10 -0500
parents 07cd87e94fbe
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Cconverts the tabular pileup output from samtools mpileup to a VCF file.  
Filters on read coverage, base quality and the frequency of a variant.  
The VCF info is populated with a SAF tag that give the specific frequency (0 - 1) of a variant being observed.
This is used for filtering in the mmuff ( Missense Mutation and Frameshift Finder) workflow.
The VCF ID field can be optionally set, which can be used with SnpSift annotate or SnpSift filter.