The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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SAMTOOLS-0.1.19 mpileup raw-vcf-out 

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From a BAM file it prepares a list of variant candidates in VCF format, ready for downstream filtering.

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Quick Start

Test Data

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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.

This is the same as running this command:

samtools mpileup -Iuf tair10genome.fas s_3_tair10srt.bam | bcftools view -vcg - > 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

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