Questions tagged [bwa]

bwa (Burrows-Wheeler Aligner) is a software for aligning reads obtained with Next Generation Sequencing.

Filter by
Sorted by
Tagged with
18 votes
2 answers
10k views

Obtaining uniquely mapped reads from BWA mem alignment

This is based on a question from betsy.s.collins on BioStars. The original post can be found here. Does anyone have any suggestions for other tags or filtering steps on BWA-generated BAM files that ...
user avatar
  • 11.8k
12 votes
2 answers
3k views

Difference between BWA-backtrack and BWA-MEM

Many of my colleagues recommend I use BWA-MEM instead of regular old BWA. The problem is I don't understand why and reading the BWA man page doesn't seem to help the matter. What is the difference ...
user avatar
6 votes
1 answer
449 views

Why most aligners do not output the "X" CIGAR operation?

As I read the SAM spec, the "X" CIGAR operator represents a mismatch. This seems useful as we can know where are the mismatches without looking at the reference genome. However, many popular aligners ...
user avatar
  • 777
1 vote
2 answers
505 views

How BWA generate index files?

I need to know how BWA generate bw and sa in less memory usage. I didn't find details in the original paper. Do they save all rotations temporary ? I need to know do BWA stores all rotations so that ...
user avatar
  • 175
15 votes
1 answer
4k views

Why is bwa-mem the standard algorithm when using bwa?

The industry standard for aligning short reads seems to be bwa-mem. However, in my tests I have seen that using bwa backtrack (bwa-aln + bwa-sampe + bwa-samse) performs better. It is slightly slower, ...
user avatar
  • 8,161
14 votes
1 answer
3k views

How does the BWA-MEM algorithm assign its mapping qualities?

Is there any resource (paper, blogpost, Github gist, etc.) describing the BWA-MEM algorithm for assigning mapping qualities? I vaguely remember that I have somewhere seen a formula for SE reads, which ...
user avatar
13 votes
4 answers
563 views

Library for computing BWT-based alignments

I am writing a software tool to which I would like to add the ability to compute alignments using the efficient Burrows-Wheeler Transform (BWT) approach made popular by tools such as BWA and Bowtie. ...
user avatar
2 votes
1 answer
426 views

Mark BWA-SW split alignments in output for long reads

Is there a way to remove split alignments of single-end long reads from BWA-SW output? BWA-MEM has an option to include or flag split alignments in the result, but it seems BWA-SW method include them ...
user avatar
1 vote
1 answer
4k views

Samtools Index: Chromosome Blocks not Continuous

I am working with short-read whole-genome sequences from the NCBI's SRA. I have aligned and sorted all of my short-read sequences and am attempting to index each sequence into .bai format using ...
user avatar
0 votes
2 answers
57 views

Variant calling for a subset of genes using whole gneome sequencing data

I have few 100 raw fastq files from whole-genome sequencing data and I would like to map these files to a set of genes only (and not whole genome) so as to find SNP's associated with them. Can anyone ...
user avatar