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Repository pileup_to_vcf
Name: pileup_to_vcf
Owner: jjohnson
Synopsis: convert a samtools mpileup pileup to vcf
converts the 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.
Link to this repository revision: https://toolshed.g2.bx.psu.edu/view/jjohnson/pileup_to_vcf/07cd87e94fbe
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf
Type: unrestricted
Revision: 8:07cd87e94fbe
This revision can be installed: True
Times cloned / installed: 835

Repository README files - may contain important installation or license information

Readme files
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.

Contents of this repository

Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Name Description Version Minimum Galaxy Version
Converts a pileup to VCF with filtering 2.1 any

Categories
Convert Formats - Tools for converting data formats
SAM - Tools for manipulating alignments in the SAM format
Variant Analysis - Tools for single nucleotide polymorphism data such as WGA