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).
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Samtools_mpileup.
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.
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
Expect 'filtered_alignments.sam' as output.