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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
children
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8:07cd87e94fbe 9:c0a6e8f595ec
1 Cconverts the tabular pileup output from samtools mpileup to a VCF file. 1 Cconverts the tabular pileup output from samtools mpileup to a VCF file.
2 Filters on read coverage, base quality and the frequency of a variant. 2 Filters on read coverage, base quality and the frequency of a variant.
3 The VCF info is populated with a SAF tag that give the specific frequency (0 - 1) of a variant being observed. 3 The VCF info is populated with a SAF tag that give the specific frequency (0 - 1) of a variant being observed.
4 This is used for filtering in the mmuff ( Missense Mutation and Frameshift Finder) workflow. 4 This is used for filtering in the mmuff ( Missense Mutation and Frameshift Finder) workflow.
5 5 The VCF ID field can be optionally set, which can be used with SnpSift annotate or SnpSift filter.