BWA-MEM FASTQ Read Mapper v1.3

What does this app do?

This app maps FASTQ reads (paired or unpaired) to a reference genome with the BWA-MEM algorithm.

What are typical use cases for this app?

This app can be used to map reads to a reference genome, which is a typical step in most bioinformatics analyses. It is suitable as a first step if you are planning on performing downstream variation calling with GATK, or any other analysis which requires mappings.

This app uses the BWA (Burrows-Wheeler Alignment Tool) software package. BWA includes three algorithms (BWA-backtrack, BWA-SW and BWA-MEM), but this app is specifically using the BWA-MEM algorithm.

The BWA-MEM algorithm is suitable for read lengths ranging from 70bp to 1Mbp. Compared to BWA-backtrack, it has better performance for 70-100bp Illumina reads; compared to BWA-SW, it is faster and more accurate if the reads are of high-quality.

What data are required for this app to run?

This app requires reads files in gzipped FASTQ format (*.fastq.gz or *.fq.gz), such as those typically produced by Illumina instruments. A single file is needed for unpaired reads, and two files (left and right read mates) are required for paired reads.

The app also requires a reference genome sequence index. This must be a gzipped tar archive file (*.bwa-index.tar.gz) containing all the sequence index files as previously output by the BWA indexer. (Indexing is an one-time operation that needs to be performed to a reference genome sequence in order for it to be usable by BWA. If you have created your own BWA index outside of DNAnexus, place all the index files in a gzipped tar archive and provide that as the input; if you have a reference genome sequence in FASTA format, you can index it with the BWA FASTA Indexer app). Some pre-indexed genomes are also available as suggested inputs. See also 'which human reference sequence should I use?' on DNAnexus Answers.

If you will be using the mappings to perform variation calling, we encourage you to provide the correct read group information, and in particular to enter a read group sample. (The default behavior is to add a read group named after the input file, assign the value ILLUMINA to the read group platform, and the value 1 to the read group sample).

What does this app output?

This app outputs the mappings, as a coordinate-sorted BAM file (*.bam). An associated BAM index file (*.bai) is also generated.

Custom modifications

Within the designated output folder the bam and bai files are output within a folder /output

How does this app work?

This app uses the BWA-MEM algorithm from the BWA software package. For general information, consult the BWA manual at:

http://bio-bwa.sourceforge.net/bwa.shtml

This app performs the following steps:

• Mapping with bwa mem.
• Conversion to BAM with samtools view.
• Sorting with samtools sort.
• Indexing with samtools index.