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 1.7 view Filter by region

With no options or regions specified, prints all alignments in the specified input alignment file. You may specify one space-separated region after the input filename to restrict output to only those alignments which overlap the specified region. Use of region specification requires a coordinate-sorted and indexed input file (in BAM or CRAM format).

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 -> Samtools_mpileup.

Input File(s)

Use ex1.bam from the directory above as bam input

use ex1.bam.bai as the bam index file

use ex1.fa from the directory above as reference sequence.

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.

  • Enter seq1:1-100 in the 'region' field

Output File(s)

Expect 'filtered_alignments.sam' as output.

Tool Source for App

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