Find SNPS - mpileup

Find SNPS Samtools 1.7 mpileup

Quick Start

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> find snps.

Input File(s)

s_3_tair10srt.bam and tair10genome.fas from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

  • Default parameters only, with the Output.vcf name changed to s_3_tair10.vcf.

Output File(s)

For the test case, the output file you will find in the example_data directory is named s_3_tair10.vcf.

Tool Source for App