Mercurial > repos > blankenberg > naive_variant_caller

comparison tools/naive_variant_caller.xml @ 11:8af4e7a4d041

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Add upgrade recommended message.
author Daniel Blankenberg <dan@bx.psu.edu>
date Thu, 17 Sep 2015 14:22:52 -0400
parents 4fab5fce1adb
children ac0235d2d459
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10:907b40517289 11:8af4e7a4d041
120 </inputs> 120 </inputs>
121 <outputs> 121 <outputs>
122 <data format="vcf" name="output_vcf" /> 122 <data format="vcf" name="output_vcf" />
123 </outputs> 123 </outputs>
124 <help> 124 <help>
125 .. class:: warningmark
126
127 Upgrading to version 0.0.2 is recommended.
128
129 ------
130
125 **What it does** 131 **What it does**
126 132
127 This tool is a naive variant caller that processes aligned sequencing reads from the BAM format and produces a VCF file containing per position variant calls. This tool allows multiple BAM files to be provided as input and utilizes read group information to make calls for individual samples. 133 This tool is a naive variant caller that processes aligned sequencing reads from the BAM format and produces a VCF file containing per position variant calls. This tool allows multiple BAM files to be provided as input and utilizes read group information to make calls for individual samples.
128 134
129 User configurable options allow filtering reads that do not pass mapping or base quality thresholds and minimum per base read depth; user's can also specify the ploidy and whether to consider each strand separately. 135 User configurable options allow filtering reads that do not pass mapping or base quality thresholds and minimum per base read depth; user's can also specify the ploidy and whether to consider each strand separately.