Create BAM from SAM file

Create BAM from SAM file is based on samtools. It uses the view and index functions of samtools to convert a SAM sequence alignment file into a coordinate-sorted, indexed binary BAM file.

Quick Start

• To use Create BAM from SAM file, upload your data in SAM format.
  • Your SAM file must have a header with @SN entries describing all the contigs or chromosomes referenced by the alignments.
• Resources: SAMTools Manual

Test Data

Input

• Use read1.fq-read2.fq.sam from http://mirrors.iplantcollaborative.org/example_data/create_bam_from_sam/read1.fq-read2.fq.sam as a test input file.

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, no further configuration needed.

Output

• Expect a sorted BAM file (filename.sorted.bam) and its index (filename.sorted.bam.bai) as output. The results of the test case can be found in the following files:
  • http://mirrors.iplantcollaborative.org/example_data/create_bam_from_sam/read1.fq-read2.fq.sam.sorted.bam (BAM file)
  • http://mirrors.iplantcollaborative.org/example_data/create_bam_from_sam/read1.fq-read2.fq.sam.sorted.bam.bai (index)

Tool Source for App

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