Question 1

What types of data does BWA work with?

Accepted Answer

BWA works with various types of DNA sequence data, including Illumina, 454, IonTorrent, PacBio, and Oxford Nanopore reads. The optimal algorithm and settings may vary depending on the data type and read length.

Question 2

Why does a read appear multiple times in the output SAM?

Accepted Answer

BWA-SW and BWA-MEM perform local alignments. If there is a translocation, a gene fusion, or a long deletion, a read bridging the breakpoint may have two hits, occupying two lines in the SAM output.

Question 3

Does BWA work on reference sequences longer than 4GB in total?

Accepted Answer

Yes, BWA can handle reference sequences longer than 4GB.

Question 4

Why can one read in a pair have high mapping quality but the other has zero?

Accepted Answer

This can occur due to various reasons, such as adapter contamination, poor quality in one of the reads, or structural variations.

Question 5

How can a BWA-backtrack alignment stand out of the end of a chromosome?

Accepted Answer

This is usually due to issues with the reference genome or alignment parameters. Ensure the reference genome is correctly formatted and the alignment parameters are appropriate for the data.

Question 6

Can I just run BWA-MEM against GRCh38+ALT without post-processing?

Accepted Answer

Running BWA-MEM against GRCh38+ALT requires careful post-processing to handle the alternative contigs appropriately. Consider using specialized tools for ALT-aware alignment.

Question 7

Why does BWA use a lot of memory?

Accepted Answer

BWA uses a lot of memory because it needs to load the entire reference genome and its FM-index into memory for efficient alignment. The memory usage depends on the size of the reference genome.

Burrow-Wheeler Aligner (BWA)

Should you use Burrow-Wheeler Aligner (BWA)?

Overview

FAQ

Pricing

Pros & Cons

Reviews & Ratings